SEQanswers

New Member

pajif84530 — Fri, 13 May 2022 10:56:52 GMT

Hi nice to meet you all , and looking forwed posting and helping

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Bộ sưu tập mẫu nhẫn cưới đẹp được ưa th�ch nhất bởi c�c cặp đ�i

kimcuongtierra — Fri, 13 May 2022 09:45:31 GMT

Nếu như trong qu� khứ, những mẫu nhẫn cưới v�ng trơn truyền thống l� kiểu nhẫn �quốc d�n" th� ng�y nay, ch�ng ta đ� được chứng kiến sự l�n ng�i của h�ng loạt thiết kế mới như nhẫn cưới hiện đại độc đ�o, ph� c�ch hay nhẫn cưới kim cương đẳng cấp, thanh lịch... Vậy những mẫu nhẫn cưới đẹp n�o đang l� hot trend được y�u th�ch nhất bởi c�c cặp đ�i trẻ hiện đại ng�y nay? Mời bạn c�ng ch�ng t�i kh�m ph� trong b�i viết dưới đ�y nh�.

https://www.tierra.vn/goc-bao-chi/ya...ac-cap-doi-268
Cặp nhẫn cưới hiện đại NCC2011

Lấy cảm hứng từ sự h�a quyện v� gắn b� giữa hai t�m hồn, mẫu nhẫn cưới NCC2011 c� điểm nhấn l� đường gờ nổi vắt ch�o qua đai nhẫn trơn đầy tinh tế. Nhẫn cưới nữ c� dải kim cương thi�n nhi�n lấp l�nh sang trọng v� qu� ph�i. Nhẫn cưới nam đai bản d�y mạnh mẽ với một mảng chải xước nổi bật tr�n bề mặt trơn. Đ�y lu�n l� một trong những mẫu nhẫn cưới đẹp rất được l�ng c�c cặp đ�i hiện đại, trẻ trung v� thanh lịch.

https://www.tierra.vn/goc-bao-chi/ya...ac-cap-doi-268
Cặp nhẫn cưới truyền thống NCC1012

Thiết kế theo phong c�ch tối giản tới tuyệt đối, cặp nhẫn cưới đẹp NCC1012 c� đai nhẫn trơn b�ng, kh�ng đ�nh nạm kim cương, ri�ng nhẫn cưới nữ c� đ�nh kim cương tấm tạo điểm nhấn kh�c lạ. Tuy l� kiểu nhẫn cưới truyền thống nhưng NCC1012 lại sử dụng đai nhẫn với mặt cắt đa gi�c, mang lại n�t trẻ trung hợp với c�c cặp đ�i trẻ hiện đại, năng động.

Cặp nhẫn cưới hiện đại NCC2013

Cặp nhẫn cưới hiện đại NCC2013

Tối giản nhưng đầy ấn tượng như một t�c phẩm nghệ thuật, mẫu nhẫn cưới NCC2013 sử dụng đai nhẫn ch� nh�m l�m nền cho vi�n kim cương Fancy shape độc đ�o nằm trong chấu Channel. Mẫu nhẫn cưới đẹp với m�u sắc trẻ trung, thời thượng n�y sẽ rất ph� hợp cho những kh�ch h�ng trẻ c� gu thẩm mỹ hiện đại, nh�n thấy được vẻ đẹp từ những thiết kế giản đơn v� c� đọng nhất.

https://www.tierra.vn/goc-bao-chi/ya...ac-cap-doi-268
Cặp nhẫn cưới hiện đại NCC2029

L� một thiết kế với đai Twist c�ch điệu, cặp nhẫn cưới hiện đại NCC2029 c� đường gờ nổi vắt ch�o qua đai nhẫn tạo th�nh hiệu ứng thị gi�c kh� độc đ�o. Đường gờ nổi n�y tr�n đai nhẫn cưới nam c� bề mặt phun c�t c� t�nh c�ng vi�n kim cương chủ đ�nh theo kiểu chấu Flush, trong khi ở nhẫn cưới nữ l� dải kim cương tấm đ�nh kiểu Shared Prong. C�c cặp đ�i trẻ đang t�m kiếm một phong c�ch mới mẻ v� bắt mắt chắc chắn kh�ng n�n bỏ qua cặp nhẫn cưới đẹp n�y.

Cặp nhẫn cưới hiện đại NCC2034

https://www.tierra.vn/goc-bao-chi/ya...ac-cap-doi-268
Những năm gần đ�y, sức h�t của m�u v�ng hồng ngọt ng�o, ấm �p v� thời trang ng�y c�ng được y�u th�ch. Mẫu nhẫn cưới NCC2034 c� nhẫn cưới nữ sử dụng m�u v�ng hồng l�m điểm nhấn nổi bật với thiết kế đai c� một mặt cắt phẳng kh� lạ mắt v� c� t�nh, kim cương tấm được đ�nh bằng chấu bi nh�n như một ng�i sao lấp l�nh vụt ngang qua bầu trời đ�m. Nhẫn cưới nam mang thiết kế gần tương tự nhưng kim cương được đ�nh trong một mảng tam gi�c g�c cạnh hơn v� bản đai d�y mạnh mẽ. NCC2034 l� một trong những mẫu nhẫn cưới đẹp c� thể t�n l�n vẻ sang trọng, qu� ph�i của người đeo.

Cặp nhẫn cưới hiện đại NCC2040

Cặp nhẫn cưới hiện đại NCC2040

Ở mẫu nhẫn cưới hiện đại NCC2040, c�c nh� thiết kế đ� sử dụng đai nhẫn dạng Twist đan v�o nhau như một n�t thắt tượng trưng cho mối li�n kết v� gắn b� bền chặt giữa hai vợ chồng. Nhẫn cưới nữ được đ�nh xo�n đối xứng trong khi nhẫn cưới nam chỉ sử dụng đai trơn b�ng đơn giản. Mẫu nhẫn cưới đẹp ngọt ng�o v� � nghĩa n�y sẽ l� m�n t�n vật t�nh y�u kh�ng thể ho�n hảo hơn d�nh cho c�c cặp đ�i hiện đại, l�ng mạn.

https://www.tierra.vn/goc-bao-chi/ya...ac-cap-doi-268
Cặp nhẫn cưới kim cương NCC3004

D�nh cho c�c cặp đ�i y�u th�ch phong c�ch truyền thống, đơn giản, mẫu nhẫn cưới NCC3004 c� thiết kế tương đồng tr�n cả nhẫn cưới nam v� nhẫn cưới nữ với đai nhẫn ch� nh�m, hai viền bi đối xứng nhau c�ng vi�n kim cương chủ tr�n kinh điển, tạo n�n một cặp nhẫn cưới đẹp vừa sang trọng, vừa tinh tế, nhẹ nh�ng, kh�ng ph� trương.

https://www.tierra.vn/goc-bao-chi/ya...ac-cap-doi-268
Cặp nhẫn cưới vương miện NCC8003

Được lấy cảm hứng từ vương miện của c�c vị vua v� nữ ho�ng trong lịch sử, cặp nhẫn cưới vương miện NCC8003 bao gồm nhẫn cưới nữ d�ng chữ V c�ch điệu, đai nhẫn thanh mảnh đ�nh kim cương tấm kiểu Half Eternity thanh lịch v� tinh tế. Nhẫn cưới nam đai bản rộng đầy nam t�nh, bề mặt kim loại trơn b�ng đơn giản với điểm nhấn l� mảng khuyết khớp với d�ng vương miện của nhẫn cưới nữ, thể hiện � nghĩa hai người l� mảnh gh�p c�n thiếu của cuộc đời nhau. Thiết kế nhẫn cưới đẹp n�y mang đến cho người đeo sự sang trọng, qu� ph�i, rất ph� hợp cho những cặp đ�i ưa th�ch phong c�ch ho�ng gia.

Cặp nhẫn cưới Eternity NCC0004

Cặp nhẫn cưới Eternity NCC0004

L� một trong c�c biến thể của kiểu nhẫn cưới Eternity nguy�n bản, cặp nhẫn cưới NCC0004 chỉ sử dụng kim cương tấm đ�nh tr�n một nửa đai của nhẫn cưới nữ, được gọi l� Half eternity. Nhẫn cưới nam xử l� bề mặt phun c�t kết hợp c�ng vi�n kim cương chủ d�ng tr�n kinh điển. Chi tiết viền bi xuất hiện tr�n cả hai chiếc nhẫn cưới tạo n�n điểm nhấn nhẹ nh�ng v� tinh tế. Cặp nhẫn cưới NCC0004 với � nghĩa tượng trưng cho một t�nh y�u vĩnh cửu l� mẫu nhẫn cưới đẹp d�nh cho c�c cặp đ�i y�u th�ch phong c�ch trẻ trung v� nhẹ nh�ng.

https://www.tierra.vn/goc-bao-chi/ya...ac-cap-doi-268
Cặp nhẫn cưới Eternity NCC0010

Sử dụng thiết kế Eternity nguy�n bản với đai đ�nh nạm to�n bộ bằng kim cương tấm, cặp nhẫn cưới Eternity NCC0010 sở hữu vẻ ngo�i trẻ trung, hiện đại v� sang trọng. Nhẫn cưới nam bề mặt kim loại chải xước lạ mắt, sử dụng viền bi đối xứng c�ng vi�n chủ tr�n lớn l�m điểm nhấn. Nhẫn cưới nữ gắn kim cương tấm Eternity bằng kiểu chấu chung Shared Prong nhẹ nh�ng, nữ t�nh. Với � nghĩa hướng về sự vĩnh cửu của t�nh y�u, cặp nhẫn NCC0010 lu�n l� mẫu nhẫn cưới đẹp ưa th�ch của c�c cặp đ�i trẻ với phong c�ch thanh lịch, tinh tế.

Li�n hệ với Tierra để t�m kiếm m�n trang sức trong mơ của bạn tại https://www.tierra.vn/

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sekar — Thu, 12 May 2022 10:09:11 GMT

List out top 5 search engines in India

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Postdoctoral Position | Computational RNA Biology | University of Arizona, Phoenix

reficul — Tue, 10 May 2022 18:54:22 GMT

My lab is looking for a strong PostDoc in RNA biology with a focus computational RNA biology and bioinformatics in the cardiovascular system. We are part of the new Translational Cardiovascular Research Center (TCRC) of the University of Arizona College of Medicine - Phoenix. Our lab is located in the pulsating new downtown of Phoenix, Arizona.

Interested? Find out more about our lab at https://jakobilab.org or message me!

Direct link to job posting: https://links.jakobilab.org/postdoc_seqanswers

What we offer:

The University of Arizona College of Medicine � Phoenix (COM-P) is seeking a highly motivated candidate for the full-time position of Postdoctoral Research Associate in Dr. Tobias Jakobi's laboratory. The lab focuses on the interplay of coding and non-coding RNAs, such as the novel class of circular RNAs in heart disease. To study these RNAs, we develop new computational open-source tools that can be used by our lab as well as other researchers in their field of interest. The successful candidate will contribute towards research and research-related service in the area of translational cardiovascular research. The successful Postdoctoral candidate should be organized, detail oriented, productive and be able to work independently as well as with others. The Postdoctoral candidate will benefit from the interaction with the diverse and interdisciplinary environment at the University of Arizona College of Medicine - Phoenix.

The University of Arizona College of Medicine � Phoenix anchors the 28-acre Phoenix Biomedical Campus in the heart of the Valley of the Sun. The College inspires and trains individuals to become exemplary physicians, scientists and leaders who are life-long learners and inquisitive scholars. The Phoenix Biomedical Campus embodies the University�s priorities of engagement, partnership, innovation, and synergy in its world-class academic and research initiatives, with clinical facilities throughout Greater Phoenix.

Outstanding UA benefits include health, dental, vision, and life insurance; paid vacation, sick leave, and holidays; UA/ASU/NAU tuition reduction for the employee and qualified family members; access to UA recreation and cultural activities; and more!

The University of Arizona has been recognized for our innovative work-life programs.

Your Qualifications:

- Knowledge of the biological sciences.
- Experience in computational biology / bioinformatics data analysis methods.
- Expertise in working with the Linux/Unix command line (bash, make, software management).
- Proficiency in handling large-scale scientific data sets and cluster computing environments.
- Knowledge of reproducible and scalable research such as software version control (git); knowledge of container solutions (docker, singularity, conda) is a plus.
- Proficiency in Python and R.
- Solid background knowledge in RNA biology.
- Experience in molecular biology is a plus.
- Ability to independently develop reports and manuscripts and present findings in tabular, oral, written, and graphic formats.

Interested? Apply now at https://links.jakobilab.org/postdoc_seqanswers!

Attached Images

teaser.jpeg (144.8 KB)

What we can learn from FastQC reports

Alexsongh — Sat, 07 May 2022 21:20:58 GMT

Thank you for your reply! If I want to do assembly afterwards, do I need to trim and filter the reads? Thank you very much!

Computer Suggestions for Minion Mk1c

contranata — Wed, 04 May 2022 15:55:04 GMT

Hi,

We are looking to buy a computer since our IT department figured it'll be easier this way. I was wondering what type of computer system has worked best for you? We are currently in the looks of doing single cell genomics and cDNA analysis. It would be nice to know the general scope of how everyone is using nanopore (for what purpose) and which type of computer has worked best for it. Thank you in advance!

SNPsaurus offers Illumina bacterial genome sequencing service

vivianshaw — Wed, 04 May 2022 12:27:11 GMT

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Whole Genome Sequencing (WGS) Service for Cancer

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Whole genome sequencing (WGS) is a key driver for many medical research projects in cancer and complex genetic disorders. Creative Biolabs has established the high-throughput SuPrecision� platform for large-scale sequencing services. Based on this advanced platform, we can provide the most comprehensive cancer WGS sequencing bioinformatics analysis for our global customers.

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RNA size selection

lre1234 — Tue, 03 May 2022 18:55:02 GMT

Hi All,
We are trying to follow-up on some small RNA-sequencing that we have done. We would like to do some northern blots on the RNA and probe for some short RNA molecules that we found (non miRNAs). The typical short RNA-seq library prep protocol does a size section after the adapters have been added and after converted to cDNA. Here, we would like to do a size selection on total RNA first, then do a northern blot. Also, we would need to use a substantially larger amount of RNA than you would for a sequence library. So, essentially, does anyone have a protocol to take a large amount of RNA (>10ug) and size select it for only those molecules <70nts long?

Thanks

New user here so just to introduce myself :)

nithi — Tue, 03 May 2022 11:56:17 GMT

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PrecisionFDA's NCTR Indel Calling from Oncopanel Sequencing Data Challenge

sarah_p — Mon, 02 May 2022 22:05:32 GMT

The challenge is now live! Find out more about Phase 1 at: https://go.usa.gov/xumhS

Quote:

Originally Posted by sarah_p (Post 242402)

The primary goal of the NCTR Indel Calling from Oncopanel Sequencing Data Challenge is to encourage the bioinformatics community to develop, validate, and benchmark indel calling pipelines to identify indels in Oncopanel sequencing datasets. Given the widely recognized impact of indels on protein coding and function, it is tremendously crucial that the tools for indel-calling be rigorously evaluated and optimized.

The submission period for Phase 1 opens on May 2nd and closes on July 8th. The optional Phase 2 submission will follow from July 11th through July 26th. Challenge top performers will be publicly recognized and invited to contribute to a manuscript and a webinar describing the challenge and results. To pre-register, visit the site: https://go.usa.gov/xuZYR

Why there are some nonsense repetitive reads shown in the sequencing result fasta?

btphzxc — Mon, 02 May 2022 19:06:59 GMT

When I check the reads included in the fasta file generated by MiSeq platform, I found some reads like this:
GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG
or this:
GTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTG

I BLAST them in the NCBI dataset, but no hit was obtained, meaning they are not actual sequences.
Does anybody know why such reads were present in the MiSeq fasta file? Thank you.

Methylation Specific Bisulfite-Seq Library Prep Kit

BioDynami — Mon, 02 May 2022 18:12:44 GMT

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Utilizing Innovations in Single-Cell Sequencing

scienceguy — Mon, 02 May 2022 16:39:07 GMT

Upcoming Webinar

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Introducing BBDuk: Adapter/Quality Trimming and Filtering

trotos — Mon, 02 May 2022 12:34:28 GMT

Quote:

Originally Posted by GenoMax (Post 217998)

@horvathdp: You can provide NEBnext primers in a separate file as multi-fasta sequence. Then use that file with bbduk.sh. Also with paired-end reads use options "tpe tbo" to get residual bases at end of reads.

If I may do a follow-up:
I will like to use BBduk for trimming adapters form the NEBBext single cell/ Low input kit.
NEB recommends using Flexbar. The adapters used are as on the previous post. And mor in detail HERE In this page they recommend using FlexBar. Flexbar first will firstly remove the switching oligo and also G and T homopolymers using the following options:

Code:

Homopolymers adjacent to the template-switching oligo are trimmed as well, as specified by --htrim* options. G and T homopolymers are trimmed (--htrim-left GT --htrim-right CA). Homopolymer length to trim is 3-5 for G, and 3 or higher for T (--htrim-min-length 3 --htrim-max-length 5 --htrim-max-first).

Keeping a short minimum read length after trimming (--min-read-length 2) keeps informative long reads, whose mates may be short after trimming.

Then in a separate step it will proceed on trimming the illumina adapters.

I am unsure how I can adjuste BBduk for those Homopolymers

Quote:

Originally Posted by GenoMax (Post 217998)

It is mentioned that the adapters should be provided in a separate file. This will include both the switching primer and the illumina adapters, as described in the fasta files from the github link? And how BBduk handles this 2 step process?

Thank you all in advance.

Cleaning up ~12,000 bp product

BioDynami — Mon, 02 May 2022 11:54:25 GMT

SPRI Beads (DNA & RNA Purification)
https://biodynami.com/product/spri-b...-purification/

Features:

Save 75% of the cost
Purification of DNA and RNA
- DNA fragments > 100 bp
- RNA fragments > 200 nt
Removal of unwanted components and impurities

Tanric

Anamika Pandey — Mon, 02 May 2022 05:47:13 GMT

How can i download the data from TANRIC database?

Unexpected kmer occurence distribution across 10 bacterial genomes

jmartin — Fri, 29 Apr 2022 21:20:32 GMT

I'm trying to identify unique regions across a large collection of bacterial genomes and my first step is to use tallymer (from the genometools package) to identify unique kmers across the entire db. I started out with a small set of 10 genomes (to familiarize myself with the tools) and after building the suffix index I ran tallymer occratio to get a distribution of unique and non-unique kmers per mer-size, but the distribution is sort of opposite what I expected:

# distribution of unique mers
10 520
11 1490
12 2403
13 2887
14 3077
15 3151
16 3178
17 3191
18 3197
19 3200
20 3203
21 3205
22 3207

# distribution of non unique mers (counting each non unique mer only once)
10 689042
11 1306536
12 1748019
13 1944353
14 2012896
15 2034879
16 2041859
17 2044257
18 2045175
19 2045601
20 2045875
21 2046092
22 2046265

Naively I had expected to find more instances of the smaller kmers in my test set than the larger mer-sizes. That assumption was based on my thinking that as my mer-size approaches my genome size the number of possible instances goes down (down to just 1 'mer' whose size is the length of the genome).

Can anyone comment on what I am seeing based on their own experience? My assumption is based on that one very flimsy thought (a mer size of genome length can only occur once), but I wanted to make sure my results are not unexpected before moving ahead. Note that I have no reason to believe there was any problem with the execution of tallymer (or suffixerator prior to the tallymer occratio command). The jobs finished without warning or error and produced the expected outputs.

paired end mapping with one end being unique and the other end multiple

schu — Fri, 29 Apr 2022 15:33:52 GMT

Hi all,

This may be a question already and repeatedly asked before, but I could not find an answer relevant to my issue...

I would like to map human/mouse genome sequence data of paired end reads (150 bp x 2 etc.) allowing one end being "uniquely" mapped and the other end "multiply" mapped in order to increase mappability to repetitive regions.

Is this (one end uniquely and the other end multiply mapped) possible for common mapping softwares such as bowtie2, bwa etc. by properly setting some option parameters, or do I need to manually filter (by awk etc.) the output, for which I allow for multimapping reads of both ends?

Thank you for your kind help and advice in advance.

quality score issues

dubravka.pezic@labgeni.us — Fri, 29 Apr 2022 15:01:49 GMT

Hi all,

i am wondering what are possible causes of low Q30 scores, apart from overclustering?

I am working with amplicon libraries which were sequenced on MiSeq using v2 500 PE kit. I sequenced 12 libraries, all prepared simultaneously using the same method. PhiX comprised 21% of the run. The run metrics looked good with avg Q30 of 88%, and the output was very high with nearly 43 million PE reads (expected 25-30 mil). Cluster density was high, about 1,200 K/mm2 which is the upper end for this kit, but ~94% reads passed filter.
However when I ran FastQC on my samples I got very poor per base quality scores for some libraries (but not all!). For some libraries the scores were worse for Read 1, and for others for Read 2. This resulted in a lot of data being discarded.
It basically looks like Q30 data from BaseSpace (where median Q30 score is low only for late cycles for each read) does not match with quality scores given by FastQC.

I would be grateful for any insight as to why this would happen!

Many thanks,
Dubravka

Comparing loci across catalogs

akoontz11 — Thu, 28 Apr 2022 16:20:39 GMT

Hi all,

Context: I'm using the Stacks (v2.59) ref_map.pl command to analyze garden and wild samples of my species, and have aligned my paired-end RAD reads to a reference genome using GSNAP. The goal is to measure how many wild alleles are observed (captured) within garden samples. To this end, I want to generate a catalog of wild loci, a separate catalog of garden loci, and then measure the proportion of wild loci observed in the garden catalog.

My question is: how can I match RAD loci that were generated in separate catalogs? For instance, can I use adegenet to read in the files generated by Stacks and match the names of loci, since both garden and wild samples are aligned to the same reference (using the same parameters)?

My preference is to do this in R (ideally with adegenet, but open to other approaches). If not, is there a way I could just compare across 2 loci catalogs (i.e. find matches between two .fa.gz files)?

Thanks for any tips!

Hello guys!

Aftershock — Thu, 28 Apr 2022 12:23:20 GMT

Hello everyone!

I'm glad to be here as a part of the community. I hope I will be useful here :)

Bcftools installed via Cygwin plugin error

audreyrosemary — Wed, 27 Apr 2022 19:51:40 GMT

Hi! I am trying to look at several genomes of different individuals of the same species and call the SNPs for each genome using bcftools. I installed bcftools via Cygwin terminal on Windows 10, but I keep receiving the following error when I am trying to use the plugins (count, etc.):

Code:

No functional bcftools plugins were found in

        BCFTOOLS_PLUGINS="/usr/local/libexec".



- Is the plugin path correct?



- Run "bcftools plugin -l" or "bcftools plugin -lvv" for a list of available plugins.

When I run "bcftools plugin -l" I get the same message. The original bcftools installation folder is in a different place compared to the installed bcftools that are in usr/local/libexec (the actual program is in usr/local/bin), so I tried to export the path to the plugins to the plugin folder in the original bcftools directory which didn't help. I also tried to leave the plugins path to "/usr/local/libexec" and manually copy-paste the plugins folder in there, but that issued again the error above. The plugins folder is in the path mentioned, but it is either not recognized or doesn't contain functional plugins. When I try to ask why does the count plugin specifically not work, I get the following message:

Code:

$ bcftools plugin count -vv

plugin directory /usr/local/libexec .. ok

/usr/local/libexec/count.cygdll:

        dlopen   .. No such file or directory

count:

        dlopen   .. No such file or directory



The bcftools plugin "count" was not found or is not functional in

        BCFTOOLS_PLUGINS="/usr/local/libexec".



- Is the plugin path correct?



- Run "bcftools plugin -l" or "bcftools plugin -lvv" for a list of available plugins.



Could not load "count".

The count.cygdll and count.c files do exist though in the plugins directory so I am confused of why the plugins are not recognized. I would deeply appreciate any input!

Furthermore, I would also appreciate any separate advice about how to align whole-genome assemblies to one reference genome in order to generate the required aligned .SAM file as input for bcftools. I know how to align short sequences, but I don't know for sure how to employ that for an entire genome.

Thank you very much!

Basemean threshold

suzie123 — Wed, 27 Apr 2022 10:12:42 GMT

I have an rna seq dataset and I am using Deseq2 to find differentially expressed genes between the two groups. However, I also want to remove genes in low counts by using a base mean threshold. I used pre-filtering to remove any genes that have no counts or only one count across the samples, however, I also want to remove those that have low counts compared to the rest of the genes. Is there a common threshold used for the basemean or a way to work out what this threshold should be?

Thank you

BBMap (aligner for DNA/RNAseq) is now open-source and available for download.

Omri.huji — Mon, 25 Apr 2022 21:39:32 GMT

Hello Brian,

I will be glad to get your help with the next issue.
I mapped a large DB of reads(over 100K) against the human genome, and found different results between bbmap's and bbmapskimmer's mappings.

I used bbmap to map reads against hg19, then I was interested finding all the mappings over the genome- so I used bbmapskimmer.
Except this concept I do not know any main differences between bbmap and bbmapskimmer codes (am I right?).

And still, bbmap mapped 98,425 reads and bbmapskimmer mapped 107,708. While 96,987 reads are shared.
Means bbmap mapped 1,438 reads that wasn't mapped by bbmapskimmer, which did mapped another 10,721 that wasn't mapped by bbmap- some of them with perfect minid score of 1.0.
Is there any possible reason for that?

I attached SAM files, with the relevant mappings for reads with maximum minid score in each algorithem (best minid for 1,438 reads of bbmap is 0.96, and for bbmapskimmer is 1.0).

- I used the next reference genome: hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz

- All mappings were done with next parameters: minid=0.9 ambig=all

Attached Files

	bbmap_minid=0.96.sam.txt (6.1 KB)
	bbmapskimmer_minid=1.sam.txt.zip (20.3 KB)

IP Theft, Racism & Plagiarism by University of Cambridge, UK, Professor

narain — Mon, 25 Apr 2022 15:28:54 GMT

Racism & Plagiarism at Plant Sciences department, University of Cambridge, UK, with a PhD student: https://lnkd.in/d7W8Jy-k #cambridgeuniversity #phd #racism #uk University of Cambridge #plagiarism #stealing Alison Smith John Carr #university #plantscience Severin Sasso BIOGEMMA UK LIMITED Springer Nature Group

Please share: www.tinyurl.com/cambridgecase .

IP Theft, Racism & Plagiarism by University of Cambridge, UK, Professor

narain — Mon, 25 Apr 2022 15:22:31 GMT

bam2pindel Error

Lillianwu0314 — Mon, 25 Apr 2022 13:17:08 GMT

Hi all,

Very late to the party. I've been getting the same error message when trying to run bam2pindel. Has anyone managed to solve it? I emailed Kai Ye but he has yet to reply.

Online Course - A Practical Introduction to NGS Data Analysis (May 16-18, 2022)

ecSeq Bioinformatics — Mon, 25 Apr 2022 07:42:24 GMT

Online Course - A Practical Introduction to NGS Data Analysis

Quality Control, Read Mapping, Visualization and DNA Variant Analysis

When? May 16-18, 2022, 9 am - 5 pm (CEST UTC+2)

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Link? Website

In a nutshell

Learn the essential computing skills for NGS bioinformatics
Understand NGS technology, algorithms and data formats
Use bioinformatics tools for handling sequencing data
Perform first downstream analyses for studying genetic variation

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Shallow shotgun metagenomics

Rahel31 — Sat, 23 Apr 2022 14:46:53 GMT

Hi,
I am trying to switch from 16S to shotgun metagenomics, but as the number of samples is quite high (several hundreds of human stool samples), then deep sequencing is a bit problematic price wise. I have been reading up on shallow shotgun sequencing - basically like the deep one, but you pool more samples and aim for lower number of reads per sample (half a million reads in some studies, a bit more in others). A bioinformatician I talked with said that now it should be quite reasonable as the databases for human gut microbiome are becoming rather complete, so that you don't need to assemble the genomes de novo, but could map to the genomes in existing database. Then again, a company doing metagenomics as service said that the clients are often requesting shallow shotgun metagenomics, but then are unhappy with the results...
We are aiming at having a species, hopefully sub-species resolution and as well to have functional information on the gut microbiome. Not looking at exhaustively specific genes, like AMR-genes etc...

I would really appreciate if you could you please share your experience with shallow shotgun metagenomic sequencing! What limitations did you encounter etc.
Another option would be to cut down on library preparation costs, for example by using the Hackflex protocol, but as we are not experienced in shotgun library preparation, then maybe this is more dangerous path to go down with.
Thank you in advance!

Information about Wikipedia?

StevenSperry — Sat, 23 Apr 2022 09:04:33 GMT

Wikipedia is an extremely news site that I am known for. I have used it in most of the reports that need official information as a reference, So where is the source of the official Wikipedia information and documentation? Please share with me

Priming Flongle Flowcell

d_araneda_r — Wed, 20 Apr 2022 23:31:24 GMT

Hi!
I hope you are very well, what protocols are there for priming the Flongle Flowcells?
Thanks.

Computational biologist / Bioinformatician at UT Southwestern Medical Center

xingerguan — Wed, 20 Apr 2022 19:31:05 GMT

0
5 months ago
chao.xing ▴ 20

The Bioinformatics Lab of McDermott Center for Human Growth and Development at University of Texas Southwestern Medical Center at Dallas solicits applications for Computational Biologist I & II.

Experience & Education Required

Master's or Doctor�s degree in Computer Science, Bioinformatics, Biostatistics, or Statistics.
Experienced with Linux.
Experienced with scripting languages such as R, Python and Perl.
Experience with sequencing data preferred.

Position Details Candidates will work as part of a team in Center's Bioinformatics Lab to maintain and revise reliable high performance next-generation sequencing (NGS) data analysis pipeline systems, to process/analyze data in a reliable and timely fashion. Candidates must have good customer service and communication skills with faculty scientists and sequencing core.

Perform professional work in support of scientific research using technical knowledge of software, software development, networking, and/or hardware in a complex computing environment.
Perform complex data analysis related to specialized research methodologies and results as assigned.
Develop and/or modify software to support new and ongoing research projects.
Develop and maintain complex databases to support new and ongoing research projects.
Performs other duties as assigned.

Visit us at: https://www.utsouthwestern.edu/labs/bioinformatics-lab/.

Contact: Chao Xing, Ph.D., chao.xing at utsouthwestern.edu

UT Southwestern Medical Center at Dallas is an equal opportunity employer.

Want to automate your NGS analyses and create reproducible/scalable pipelines?

ecSeq Bioinformatics — Wed, 20 Apr 2022 12:07:27 GMT

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library clean-up using AMPure XP beads

Amberlycole — Tue, 19 Apr 2022 11:41:37 GMT

Hi all,

I'm having some problem when performing library clean-up, I found when I reduced the bead ration from the recommended 0.8X twice to 0.7X twice, I can almost remove all the adapter dimers in my library, but when I analyzed the sequencing data from such library, I found the mapping rate reduced from original 40% to less than 10%, I wondered is this because I reduced the bead ratio, which cause the loss of a good proportion of my fragment?

Thanks!

Miniseq run issues

tired_of_overclustering — Mon, 18 Apr 2022 21:53:48 GMT

Hi,
I am new to sequencing stuff by myself and till date I have ran at least 30 miniseq runs. Some runs were decent, but most of the runs over clustered in spite of quantifying libraries using NEB library quant kit. I make my own libraries using two sets of PCR and custom designed barcodes, purify and run bioanalyzer. Is there a way to troubleshoot what is exactly wrong? I did contact Illumina and they haven't given me a satisfactory answer ever. Any help would be appreciated.:(

Pooling for Oxford Nanopore Multiplex Sequencing

gringer — Thu, 14 Apr 2022 12:17:43 GMT

Literature? I don't understand what you mean by that.

I've noticed across many different runs that sequencing run performance on nanopore for the same prepared and adapted library has near-identical barcode proportions regardless of run time or platform. This is expected, given that it's essentially a random sampling device. Previously, we were doing a short 15 minute run on MinION flow cells to work out actual running barcode proportion, and using that to rebalance pools and resume sequencing with a better mix. Now, we use Flongle flow cells for the same purpose. It's a little bit more expensive in terms of run cost, but there's less sequencing wasted on poor samples, so I think it works out cheaper in terms of cost per read. It'll work regardless of the sample preparation: ligation, RNA, rapid Barcoding, cDNA,... whatever.

Nanopore sequencing is heavily affected by short reads: they're small (so move faster), and have greater numbers for the same mass (so take up more adapter during sample prep). Unfortunately, they don't show up so well on a TapeStation or gel because they have low mass, so you usually don't know how many there are until you're 10 minutes into a sequencing run.

Qubit quantification (or Quantus) is a reasonable representation of mass, but doesn't help much with molarity (which is what matters more for Nanopore sequencing). It can also be affected by contamination, un-adapted template, and RNA (if RNA concentration is sufficiently high, at least ~100x DNA concentration). It's fine for a rough guess for balancing barcodes, but the best and most repeatable statistic to use is actual read counts and proportions from a sequencing run.