Biostar News

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training handbook

updated 9 weeks ago by Biostar 2.3k • written 7.0 years ago by Istvan Albert 99k

122

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10k

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24 follow

meta biostars

updated 5 weeks ago by Ram 41k • written 11.0 years ago by Istvan Albert 99k

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7.0k

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11 follow

biostars

updated 9 months ago by Ram 41k • written 10.9 years ago by Istvan Albert 99k

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4.5k

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12 follow

publication NGS

updated 7 months ago by Ram 41k • written 6.9 years ago by David Langenberger 10k

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3.9k

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windows

updated 8 months ago by Ram 41k • written 7.7 years ago by poisonAlien ★ 3.2k

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3.7k

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meta biostars

updated 9 months ago by Ram 41k • written 8.7 years ago by Istvan Albert 99k

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genome deep-learning google

updated 6 months ago by Ram 41k • written 6.0 years ago by Hussain Ather ▴ 990

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6.2k

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gamestorming

updated 9 months ago by Ram 41k • written 11.2 years ago by Giovanni M Dall'Olio 28k

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1.3k

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6 follow

DNAseq DNA WGS

updated 5 months ago by Alex Reynolds 35k • written 5 months ago by David Langenberger 10k

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1.9k

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Transcriptomics DNA-Seq Variant-Calling RNA-Seq

4 months ago by David Langenberger 10k

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6.6k

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education

updated 9 months ago by Ram 41k • written 11.2 years ago by phcompeau ▴ 330

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3.6k

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Epigenetics Workshop Bisulfite-Sequencing

updated 8 months ago by Ram 41k • written 7.5 years ago by Adele Feuerstein ▴ 460

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13k

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7 follow

ncbi genbank pubmed command-line entrez

updated 9 months ago by Ram 41k • written 9.8 years ago by Pierre Lindenbaum 158k

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3.5k

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biostars

updated 9 months ago by Ram 41k • written 10.8 years ago by Istvan Albert 99k

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6.1k

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ncbi pubmed

updated 9 months ago by Ram 41k • written 10.1 years ago by Pierre Lindenbaum 158k

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6.9k

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9 follow

blast alignment

updated 6 months ago by Ram 41k • written 5.2 years ago by Farbod ★ 3.4k

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4.3k

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crowd-coding

updated 9 months ago by Ram 41k • written 10.4 years ago by Pierre Lindenbaum 158k

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4.4k

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github git

updated 9 months ago by Ram 41k • written 9.6 years ago by Pierre Lindenbaum 158k

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6.5k

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bisulfite-sequencing workshop epigenetics

updated 11 months ago by Ram 41k • written 8.5 years ago by David Langenberger 10k

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2.9k

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meta

updated 6 months ago by Ram 41k • written 4.6 years ago by Glory Basumata ▴ 140

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1.4k

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ensembl course training

updated 7 months ago by Ram 41k • written 6.8 years ago by Emily 23k

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3.8k

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6 follow

dna sequence research language

updated 8 months ago by Ram 41k • written 7.7 years ago by Sukhi Singh 11k

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3.2k

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ncbi eutils

updated 9 months ago by Ram 41k • written 11.0 years ago by Chris Maloney ▴ 360

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6.9k

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rRNA-depletion RNA-seq-bias

updated 9 months ago by Ram 41k • written 9.4 years ago by support ▴ 640

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3.3k

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chipseq rna

updated 9 months ago by Ram 41k • written 10.4 years ago by David Langenberger 10k

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1.9k

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NGSchool Personalised-Medicine Nanopore

updated 6 months ago by Ram 41k • written 5.5 years ago by kzkedzierska ▴ 290

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3.7k

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ensembl rest-api

updated 9 months ago by Ram 41k • written 9.1 years ago by Denise CS ★ 5.2k

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2.3k

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GSoC open-source

updated 8 months ago by Ram 41k • written 7.7 years ago by Philipp Bayer 8.1k

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7.4k

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sequencing

updated 6 months ago by Ram 41k • written 6.5 years ago by Brian Bushnell 20k

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1.4k

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statistics p-value

updated 8 months ago by Ram 41k • written 7.7 years ago by dariober 14k

1,000 results • Page 1 of 20

Recent Votes

Comment: How do I know how much memory to use when piping to with BBMap suite (OutOfMemor

A: difference between GSEA and Gene Ontology

Answer: Does the Minion demultiplex when basecalling?

the difference between the positions called by somatic caller (MuTect2) and the position called by germline caller (UnifiedGenotyper)?

A: Extract somatic mutations and germline mutations from variant calling files?

C: visualizing mutational data using Maftools for reference genome hg19

Answer: Ambient RNA removal method that generates whole (integer) counts

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Teacher to h.mon 35k

Scholar to jared.andrews07 ★ 16k

Popular Question to hkarakurt ▴ 180

Recent Replies

Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0

The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…

Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k

I modified the answer with an approach for that use case.

Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Ram 41k

OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…

Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k

Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.

Answer: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k

Given files `genes.bed` and `snps.bed`, you could do something like: ``` $ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…

Answer: How to add exon annotations to genome annotation by alex.zaccaron ▴ 380

You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…

Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k

and you got answer that should be validate (green tick), or people asked you questions but got no answers.

Comment: Annotation Visualization IGV by awhale01 • 0

Correct I have asked those questions before.

Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k

you asked questions before: review, comment and/or validate them please: https://www.biostars.org/p/9530777/ ; https://www.biostars.org/p/9…

Comment: Ambient RNA removal method that generates whole (integer) counts by EK • 0

Thanks, Jared. Sounds like rounding counts is the simplest approach for now. :)

Comment: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k

Could you tell us which sequencer you used, how you quantified your library size and concentration, and what your loading concentration was…

Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0

I should have mentioned, we ran both Read 1 and 2 well past the points of interest. For each read we ran 75 cycles.

Answer: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k

It might be because Illumina recommends 26 cycles for Read 1: https://knowledge.illumina.com/instrumentation/general/instrumentation-genera…

Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0

Yes at 5%.

Comment: Resolving over clustered NGS with Q-scores by ATpoint 78k

Has phiX been spiked in to increase nucleotide diversity.

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