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<prev • 236 results • page 1 of 8 • next >
41
votes
5
answers
19k
views
29 follow
5
answers
How to plot coverage and depth statistics of a bam file
sequencing next-gen coverage bam depth written 3.0 years ago by krithika.gu • 140 • updated 12 hours ago by bioinfo8 • 70
185
votes
11
answers
101k
views
87 follow
11
answers
Tools To Calculate Average Coverage For A Bam File?
bam coverage sequencing written 6.4 years ago by Biomed ♦ 4.2k • updated 1 day ago by bioinfo8 • 70
2
votes
1
answer
113
views
1
answer
Random downsampling without replacement in bam files only in regions with coverage>x
reads bam coverage written 8 days ago by victorv888 • 0
3
votes
2
answers
2.0k
views
5 follow
2
answers
Calculating Mapping Coverage
calculate mapping coverage tool written 3.0 years ago by Hatem Elshazly • 50 • updated 19 days ago by Brian Bushnell ♦ 12k
0
votes
0
answers
80
views
0
answers
how to analyze the distribution over each gene in different conditions?
gene coverage rna-seq written 22 days ago by Lila M • 280
1
vote
1
answer
130
views
1
answer
how to calculate coverage in bam file over a specific bed file
bedtools multicov coverage exon rna-seq written 23 days ago by Lila M • 280 • updated 23 days ago by Devon Ryan ♦ 68k
0
votes
0
answers
70
views
0
answers
Qualimap abnormally high coverage standaed deviation
bamqc coverage standard deviation written 23 days ago by chevivien • 60
0
votes
2
answers
102
views
2
answers
Tool for BAM coverage without the soft clipping base
softclipping bam coverage written 4 weeks ago by nayshool • 20 • updated 4 weeks ago by Pierre Lindenbaum ♦ 95k
2
votes
1
answer
115
views
1
answer
coverage for unique transcript and df process
R coverage data frame written 5 weeks ago by Lila M • 280 • updated 5 weeks ago by Rashedul Islam • 140
5
votes
2
answers
228
views
2
answers
read depth of a feature (e.g gene or exon)
coverage rna-seq tool written 6 weeks ago by xd_d • 40
0
votes
1
answer
130
views
1
answer
Depth of coverage in Bam file does not match depth in VCF file
indel variant calling pindel coverage igv written 7 weeks ago by jsneaththompson • 0 • updated 7 weeks ago by tangming2005 • 2.1k
7
votes
0
answers
236
views
6 follow
0
answers
What is the definition of "read depth" vs "coverage"? (again...)
read depth coverage depth written 7 weeks ago by ariel.balter • 100
22
votes
1
answer
187
views
10 follow
1
answer
Calculating Coverage Using CIGAR String
samtools coverage bamtools written 8 weeks ago by QVINTVS_FABIVS_MAXIMVS • 1.9k
6
votes
1
answer
709
views
5 follow
1
answer
bedtools coverage gives error received illegal bin number, but that number isn't in my data!
bedtools bin chip-seq coverage error written 4 months ago by tara.alpert • 0 • updated 8 weeks ago by soloway • 0
0
votes
0
answers
94
views
0
answers
actual coverage vs. macs2
macs2 coverage coveragebed written 9 weeks ago by blur • 50
1
vote
1
answer
166
views
1
answer
How to extract high coverage region from BAM?
reads ngs bam coverage mapping written 9 weeks ago by BioGeek • 80 • updated 9 weeks ago by Pierre Lindenbaum ♦ 95k
4
votes
3
answers
1.8k
views
3
answers
How do I access genome coverage using SPADES?
genome spades coverage myposts written 22 months ago by fhsantanna • 290 • updated 10 weeks ago by shenwei356 • 3.1k
0
votes
0
answers
200
views
0
answers
How to choose best covered promoters across multiple (few hundred) *.bam genomic alignments?
genome assembly bam coverage written 4 months ago by kopiamu • 0 • updated 11 weeks ago by Biostar ♦♦ 20
3
votes
2
answers
214
views
2
answers
search for low coverage regions on bam file
bedtools genomecov coverage awk written 11 weeks ago by mary • 0 • updated 11 weeks ago by Pierre Lindenbaum ♦ 95k
4
votes
1
answer
476
views
1
answer
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome tutorial samtools coverage plot written 12 weeks ago by kirannbishwa01 • 460 • updated 12 weeks ago by Pierre Lindenbaum ♦ 95k
1
vote
1
answer
145
views
1
answer
compute coverage with file.bam and bed : bedtools empty output
bedtools bed bam coverage written 12 weeks ago by noeD • 50 • updated 12 weeks ago by Devon Ryan ♦ 68k
1
vote
1
answer
135
views
1
answer
How does coverage of all contigs varies?
reads ngs coverage depth written 3 months ago by BioGeek • 80 • updated 3 months ago by h.mon ♦ 6.6k
0
votes
1
answer
242
views
1
answer
select -500 from the TSS to +500 after the TES strand +/-
strand sequencing coverage tes tss written 4 months ago by Lila M • 280 • updated 4 months ago by Alex Reynolds ♦ 19k
5
votes
0
answers
183
views
0
answers
How to split a bed file according promoter window (-30 to 300bp)
bed chip-seq coverage deeptools edit written 4 months ago by Lila M • 280
3
votes
1
answer
338
views
1
answer
understanding contig statistics
assembly mapping reads qualimap coverage spades written 4 months ago by mary • 0 • updated 4 months ago by Brian Bushnell ♦ 12k
17
votes
4
answers
4.8k
views
9 follow
4
answers
Peak Detection In Intergenic Regions In Rna-Seq Data
rna bioconductor peak-calling coverage written 7.0 years ago by Michael Dondrup ♦ 42k • updated 4 months ago by Charles Warden ♦ 4.8k
4
votes
3
answers
316
views
5 follow
3
answers
plot coverage for WES data
bam coverage plot written 5 months ago by koala • 0 • updated 5 months ago by michael.ante • 1.6k
0
votes
0
answers
280
views
0
answers
Contig's coverage and bam files.
contig coverage bam written 7 months ago by Picasa • 290 • updated 5 months ago by Biostar ♦♦ 20
2
votes
2
answers
338
views
2
answers
What is the minimum coverage adequate for variant calls from Whole Genome Sequencing data?
next-gen whole geneome seq coverage written 5 months ago by zhaoyang198691 • 0 • updated 5 months ago by apa@stowers • 320
1
vote
1
answer
359
views
1
answer
coverage on exons with bedtools genomecov
bedtools exons rna-seq coverage written 6 months ago by guillaume.rbt • 280 • updated 6 months ago by Jeffin Rockey • 360
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