coverage Posts

Latest

Open

RNA-Seq

ChIP-Seq

SNP

Assembly

Tutorials

Tools

Jobs

Forum

Planet

All »

Home

Welcome to Biostar! about • faq • rss

Community

Log In

Sign Up

Add New Post

Showing: coverage • reset

or Classic search

votes

answers

views

answers

Is is possible to find "SureSelectXT Human Methyl-Seq Capture Library" somewhere?

methyl-seq capture library ssmethylseq coverage written 29 days ago by daisy.ko • 20 • updated 22 hours ago by Biostar ♦♦ 20

votes

answers

4.0k

views

answers

How do I access genome coverage using SPADES?

genome spades coverage myposts written 3.3 years ago by fhsantanna • 410 • updated 1 day ago by DK • 70

votes

answers

124

views

answers

find coverage of specific exomes from a bam file

bedtools genomecov bam coverage bed written 12 days ago by lait • 120 • updated 12 days ago by Pierre Lindenbaum ♦ 114k

votes

answers

views

answers

how can I get the coverage over introns only in a RNA-seq experiment?

introns coverage rna-seq written 12 days ago by Lila M • 390

votes

answer

400

views

5 follow

answer

Is there any precedent for considering marked duplicates when calculating coverage in high-depth whole-exome sequencing?

exome duplicates exome-seq coverage written 6 months ago by Dan D ♦ 6.6k • updated 15 days ago by marco_ul • 0

votes

answers

137

views

answers

coverage of a SNP site?

bedtools ngs ase coverage snp written 15 days ago by Susmita Mandal • 0 • updated 15 days ago by Kevin Blighe ♦ 32k

votes

answers

6.9k

views

10 follow

answers

What Is The Fastest Method To Determine The Number Of Positions In A Bam File With >N Coverage?

bedtools depth-of-coverage bam samtools coverage written 5.5 years ago by Malachi Griffith ♦ 17k • updated 20 days ago by Paul • 1.2k

votes

answers

799

views

answers

Rtracklayer: Converting rlelist (Coverage) to bigwig

rtracklayer bigwig coverage written 2.1 years ago by datascientist28 • 350 • updated 20 days ago by Biostar ♦♦ 20

votes

answer

views

answer

What sequence has being read by IGV's 'copy sequence'

igv alignment samtools coverage read map written 22 days ago by marongiu.luigi • 330 • updated 22 days ago by h.mon ♦ 21k

votes

answer

views

answer

Is BED file generated by bametobed sorted ?

bedtools ngs bamtobed coverage sequencing written 7 weeks ago by pacman • 50 • updated 7 weeks ago by Alex Reynolds ♦ 26k

votes

answers

2.0k

views

answers

Mapping Reads Back To Assembly Contigs To Generate Pileup

pileup bwa coverage written 6.6 years ago by Sen • 0 • updated 8 weeks ago by Biostar ♦♦ 20

votes

answers

139

views

answers

Calculating breadth of coverage for TCGA Whole Exome Sequencing data

tcga coverage written 9 weeks ago by steve • 1.8k

votes

answers

1.3k

views

answers

coverage in amplicon sequecing method

coverage written 2.7 years ago by Picasa • 390 • updated 9 weeks ago by RamRS ♦ 19k

votes

answers

983

views

answers

I have some queries on coverage

rnaseq dnaseq coverage snp written 2.7 years ago by bioinforesearchquestions • 180 • updated 9 weeks ago by RamRS ♦ 19k

votes

answers

213

views

5 follow

answers

Good mean coverage but big std in coverage

bamqc rnaseq qualimap coverage written 9 weeks ago by Pin.Bioinf • 170

vote

answers

190

views

answers

what is the conventional apporach to calculate depth of coverage?

wgs dnaseq coverage snp depth written 10 weeks ago by serpalma.v • 20 • updated 10 weeks ago by finswimmer ♦ 7.0k

votes

answer

12k

views

answer

samtools bedcov vs. bedtools coverage

dna-seq coverage written 2.5 years ago by Dataman • 260 • updated 10 weeks ago by RamRS ♦ 19k

vote

answer

260

views

answer

Giga base or Giga byte

gb assembly coverage written 3 months ago by Shawrob400 • 0

votes

answers

1.6k

views

5 follow

answers

Confirming Structural Variants In The Genome

genome coverage written 6.4 years ago by Rubal7 • 700 • updated 3 months ago by Biostar ♦♦ 20

226

votes

answers

128k

views

108 follow

answers

Tools To Calculate Average Coverage For A Bam File?

bam coverage sequencing written 7.8 years ago by Biomed ♦ 4.4k • updated 3 months ago by WouterDeCoster ♦ 34k

votes

answers

3.8k

views

10 follow

answers

Visualizing Coverage Of Ngs Reads Across Reference Genome

coverage sequencing written 5.4 years ago by nicolazilio • 20 • updated 3 months ago by Biostar ♦♦ 20

votes

answers

3.9k

views

answers

Calculate percentage of bases covered less than nX in targeted sequencing experiment

ngs coverage targeted sequencing written 3.8 years ago by RamRS ♦ 19k • updated 3 months ago by toni • 2.1k

vote

answer

345

views

answer

relationship between DP and variant call quality

read depth variant quality coverage dp written 3 months ago by miaowzai • 100 • updated 3 months ago by finswimmer ♦ 7.0k

vote

answers

210

views

answers

Extract the overlap of well-covered regions across multiple samples

wgs coverage written 4 months ago by DVA • 480

votes

answers

40k

views

47 follow

answers

How to plot coverage and depth statistics of a bam file

sequencing next-gen coverage bam depth written 4.4 years ago by krithika.gu • 250 • updated 4 months ago by Fred0730 • 30

votes

answers

237

views

answers

Does samtools depth know how to handle paired-end reads

samtools coverage written 4 months ago by roy.granit • 750 • updated 4 months ago by ATpoint ♦ 9.4k

votes

answers

153

views

answers

Coverage variance and mean coverage

sequence coverage tool written 5 months ago by ash • 10 • updated 5 months ago by finswimmer ♦ 7.0k

votes

answers

217

views

answers

How many reads cover the exon per gene from a BAM? The gene (or exon) is totally covered by BAM file?

gene bam coverage written 5 months ago by Andrea Spinelli • 10 • updated 5 months ago by Devon Ryan ♦ 86k

votes

answer

310

views

answer

Formula for extracting per base read depth/per base genome coverage from a SAM file?

bedtools alignment samtools sam coverage written 5 months ago by Diploid Progenitor • 10 • updated 5 months ago by Devon Ryan ♦ 86k

votes

answers

265

views

answers

Subset BAM file based on selected coverage, PacBio reads

arrow pbalign coverage bam pacbio written 5 months ago by MyrNat • 0

Recent Votes

Recent Locations • All »

United Kingdom, 1 minute ago
India, 4 minutes ago
United States, 6 minutes ago
Canada, 9 minutes ago

Recent Awards • All »

Teacher to Pierre Lindenbaum ♦ 114k
Scholar to Pierre Lindenbaum ♦ 114k
Teacher to RamRS ♦ 19k
Scholar to RamRS ♦ 19k
Teacher to Santosh Anand • 4.2k
Scholar to Kevin Blighe ♦ 32k

Recent Replies

A: NCBI submissions: SRA and TSA by saraoppenheim • 20
Please use the link noted above (http://desalle.amnh.org/good_citizenship_rna/). We missed a typo...
C: Where does Illumina make MEGA_Consortium_v2_15070954_A2.csv available? by cpad0112 • 10k
Not an illumina link. But if you are looking for an URL and file, check this URL: http://www.we...
A: Why snpEff annotation give different names to one same gene? by jared.andrews07 • 1.5k
It's likely due to alternative transcripts of the gene, since as you said, both of these are the ...
C: NCBI submissions: SRA and TSA by cpad0112 • 10k
Link in point 1 is not working link. Currently it is directing visitors to: https://www.researchg...
A: retrieve full TCGA datasets from cBioportal with R by akshayb04 • 20
Hi There, Thank you for putting up this tutorial. It is very helpful. However, I have some queri...
C: Documentation on VCI files? Or convert VCI to VCF? by QVINTVS_FABIVS_MAXIMVS • 2.1k
Thanks a ton, this is what I was looking for.
C: Documentation on VCI files? Or convert VCI to VCF? by h.mon ♦ 21k
I think VCI is a format from the g2gtools package. It is created from vcf files. Apparently, ther...
C: Documentation on VCI files? Or convert VCI to VCF? by QVINTVS_FABIVS_MAXIMVS • 2.1k
Diversity Outbred cohort of mouse lines that are derived from 8 founder strains. These mice are e...
C: How can keep the change in my fastq file when i use grep and sed to edit it? by h.mon ♦ 21k
And adding "ILLUMINA" to the headers will make markduplicate work? Are you referring to Picard Ma...
C: How can keep the change in my fastq file when i use grep and sed to edit it? by Zeason • 0
i will try it and thanks a lot :) maybe my question is really stupid , but i really suffered from...
C: How can keep the change in my fastq file when i use grep and sed to edit it? by Zeason • 0
thank you very much ,i will try it
C: Documentation on VCI files? Or convert VCI to VCF? by h.mon ♦ 21k
Where did you obtain this file? What are the DO mouse lines?

Content

Help

About
FAQ

Access

RSS
Stats
API

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Traffic: 1242 users visited in the last hour