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<prev • 1,141 results • page 1 of 39 • next >
3
votes
2
answers
69
views
2
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How to find a variant in a particular position in a bam file only using samtools
bam samtools sam written 7 hours ago by tw617 • 30 • updated 7 hours ago by swbarnes2 ♦ 5.0k
2
votes
1
answer
53
views
1
answer
Bam file MC tag as integer
mc bam validatesamfile sam written 3 days ago by chariko • 30 • updated 10 hours ago by John Marshall • 1.5k
3
votes
1
answer
114
views
1
answer
Convert 2 SE bam to PE bam (alignment BWA mem)
alignment bwa bam written 28 days ago by mynameliuxiang • 0 • updated 1 day ago by zx8754 ♦ 6.8k
0
votes
1
answer
102
views
5 follow
1
answer
Bam header editing
header bam written 10 days ago by Huynh Nguyen • 0 • updated 9 days ago by Istvan Albert ♦♦ 79k
0
votes
0
answers
82
views
0
answers
Read In Function for BAM file processing
bam script written 13 days ago by Jonas.Koch • 0
3
votes
1
answer
146
views
1
answer
Extract coverage from each nucleotide position of a genome in a bam file
bed bam coverage written 14 days ago by MAPK • 1.4k
1
vote
0
answers
108
views
0
answers
How do get additional bam statistics
alignment samtools rna-seq bam written 14 days ago by t-jim • 20
7
votes
1
answer
212
views
6 follow
1
answer
How to report genomic intervals essentailly overlapping in all files?
bedtools bed bam written 18 days ago by bioExplorer ♦ 3.7k
2
votes
1
answer
112
views
1
answer
Find common reads between two bam files
reads bam sequencing written 18 days ago by yl2019 • 10 • updated 18 days ago by Pierre Lindenbaum ♦ 118k
9
votes
0
answers
131
views
7 follow
0
answers
Tutorial: Generating consensus sequence from bam file
fasta consensus tutorial bam written 19 days ago by finswimmer ♦ 11k • updated 19 days ago by WouterDeCoster ♦ 37k
0
votes
1
answer
108
views
1
answer
How treat a Bam file with mutiple read groups (RG)
gatk next-gen picard read group bam written 19 days ago by zamani_2012 • 0 • updated 19 days ago by Pierre Lindenbaum ♦ 118k
3
votes
1
answer
126
views
1
answer
RNA-Seq QC for aligned files (bam)
bam qc rna-seq written 20 days ago by genomics Newbie • 20 • updated 20 days ago by Friederike ♦ 3.3k
0
votes
0
answers
99
views
0
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Might @PG headers affect downstream analyses, and how can I safely remove them from a BAM file?
read groups bam @pg written 22 days ago by olikidrod • 0 • updated 22 days ago by h.mon ♦ 24k
15
votes
1
answer
356
views
1
answer
collapsing transcript expression to gene-level expression
featurecounts rna-seq bam written 23 days ago by F • 3.4k
1
vote
1
answer
115
views
1
answer
Subsampling aligned SAM/BAM files for RNA-seq analysis
downsampling bam sam rna-seq subsampling written 24 days ago by mohammedtoufiq91 • 30 • updated 24 days ago by WouterDeCoster ♦ 37k
4
votes
1
answer
106
views
1
answer
How to remove bam files that don't contain matching reads
bowtie2 bam samtools written 24 days ago by samlambrechts299 • 130 • updated 24 days ago by Pierre Lindenbaum ♦ 118k
2
votes
0
answers
145
views
0
answers
Should I remove duplicates?
duplicates next-gen bam written 27 days ago by F • 3.4k • updated 27 days ago by ATpoint ♦ 14k
1
vote
0
answers
110
views
0
answers
Seeing only "N's" in tablet genome viewer?
genome viewer bam written 28 days ago by tuj92050 • 0
2
votes
0
answers
115
views
0
answers
Extracting a chromosome from an indexed bam file?
bam samtools chromosome written 28 days ago by tuj92050 • 0
2
votes
1
answer
1.3k
views
1
answer
Bam File With Maq
bam written 7.6 years ago by Sara • 130 • updated 29 days ago by Biostar ♦♦ 20
0
votes
0
answers
135
views
0
answers
Count matrix showing different results than UCSC tracks
mm10 featurecounts bigwig bam ucsc written 4 weeks ago by raquelgarza95 • 30
0
votes
1
answer
126
views
1
answer
Convert BAM files to paired end FASTQ
fastq bam samtools written 4 weeks ago by berke.toptas • 0 • updated 4 weeks ago by JC ♦ 7.6k
3
votes
0
answers
120
views
0
answers
Remove duplicate readnames from a bam file
duplicates bam atac-seq duplicate read names written 4 weeks ago by garnerim1988 • 0
0
votes
0
answers
88
views
0
answers
From mpileup on bam files to TMB calculation, how is it done?
snps bam mutations mpileup tmb written 4 weeks ago by Pin.Bioinf • 240
0
votes
0
answers
101
views
0
answers
Fixing inconsistent flags (strand info set for only one read) between RNA-seq read pairs with samtools/picard
samtools picard fixmate rna-seq bam written 5 weeks ago by ophilia30092 • 0
0
votes
0
answers
142
views
0
answers
Understanding the SA tag, Samtools FLAG, and Chimeric Alignments
alignment bam written 5 weeks ago by nzs208 • 0
0
votes
1
answer
2.6k
views
1
answer
How do I calculate the total read depth and allele frequency using just the target bed file and aligned bam
bed frequency allele mpileup bam written 3.7 years ago by bobrowdy123 • 0 • updated 5 weeks ago by Biostar ♦♦ 20
7
votes
1
answer
123
views
1
answer
Detecting Klinefelter from genomic files
vcf fastq bam klinefelter written 5 weeks ago by paulcaiella • 0
2
votes
1
answer
109
views
1
answer
Identify deletion in multiple bam files compared to the same bacterial reference
bedtools bam written 6 weeks ago by David • 150
1
vote
0
answers
153
views
0
answers
Sub-sampling RNA-seq data
fastq bam sam rna-seq downsampling written 6 weeks ago by mohammedtoufiq91 • 30
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