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<prev • 828 results • page 1 of 28 • next >
185
votes
12
answers
101k
views
87 follow
12
answers
Tools To Calculate Average Coverage For A Bam File?
bam coverage sequencing written 6.4 years ago by Biomed ♦ 4.2k • updated 3 hours ago by bioinfo8 • 70
0
votes
0
answers
89
views
0
answers
how to adjust BAM header after extracting only mapped reads from BAM files
bam samtools written 10 hours ago by Ric • 120
4
votes
1
answer
94
views
1
answer
Extract parts of reads from BAM file that overlap a specific region of genome
alignment bam sequencing written 1 day ago by Chadi Saad • 10 • updated 23 hours ago by Pierre Lindenbaum ♦ 95k
0
votes
0
answers
100
views
0
answers
Mutect2 error - Cannot merge sequence dictionaries
wxs tcga bam mutect2 written 1 day ago by asd • 10
0
votes
0
answers
122
views
0
answers
Google Cloud - VCF Creation Support from .bam
vcf google bam cloud google genomic written 2 days ago by david.streid.nyc • 0
2
votes
2
answers
124
views
2
answers
Compute inner mate distance for paired-end reads in a bam file
paired picard bam written 3 days ago by bioinfo8 • 70 • updated 3 days ago by Devon Ryan ♦ 68k
7
votes
2
answers
210
views
2
answers
How to generate alignment report from bam files
alignment bam written 4 days ago by kin182 • 0 • updated 4 days ago by Pierre Lindenbaum ♦ 95k
2
votes
2
answers
649
views
2
answers
How to change the quality score of reads ? (quick help is appreciated)
tophat bam fastq rna-seq written 14 months ago by mbparsa • 10 • updated 5 days ago by madhu.9124 • 0
32
votes
8
answers
17k
views
10 follow
8
answers
Efficient And Fastest Way To Sort Large (>100Gb) Bam Files?
picard samtools bam sort written 5.3 years ago by Rm ♦ 7.5k • updated 5 days ago by cmdcolin • 630
2
votes
1
answer
111
views
1
answer
Random downsampling without replacement in bam files only in regions with coverage>x
reads bam coverage written 6 days ago by victorv888 • 0
8
votes
1
answer
128
views
5 follow
1
answer
BAM compression: .tar.gz = same size as before?
gz tar compression bam written 7 days ago by Marvin • 90 • updated 7 days ago by b.nota • 3.5k
4
votes
0
answers
154
views
0
answers
Paired-read alignment length from BAM/SAM file
paired-read alignment sam bam written 10 days ago by Soumitra Pal • 10
3
votes
1
answer
106
views
1
answer
samtools sorting to index a BAM file
bam samtools written 11 days ago by db3000 • 10 • updated 11 days ago by Pierre Lindenbaum ♦ 95k
0
votes
0
answers
67
views
0
answers
How to count the number of unique alignment in PE reads? How to account for unmapped mate?
genome count bam alignment written 12 days ago by kirannbishwa01 • 460
1
vote
2
answers
206
views
2
answers
differential exon usage
exon rna-seq bam written 8 weeks ago by Lila M • 280 • updated 14 days ago by kristoffer.vittingseerup • 110
2
votes
0
answers
88
views
5 follow
0
answers
Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
fastq bam samtools tutorial alignment sequence written 14 days ago by kirannbishwa01 • 460
3
votes
2
answers
136
views
6 follow
2
answers
Bam to fastq conversion is giving error?
software error genome fastq picard bam written 15 days ago by kirannbishwa01 • 460
2
votes
1
answer
120
views
1
answer
Unmapped Pairs in Bam file
assembly next-gen bam alignment written 18 days ago by user191006 • 10 • updated 15 days ago by Devon Ryan ♦ 68k
14
votes
2
answers
179
views
5 follow
2
answers
Samtools: How can I extract properly-paired QC-passed reads instead of extracting only properly-paired?
ngs bam samtools paired-end sequencing written 18 days ago by bioinfo8 • 70
0
votes
0
answers
68
views
0
answers
Trying to check plasmid alignment
plasmid bam igv written 21 days ago by gracie • 0
1
vote
1
answer
1.7k
views
1
answer
Does Markduplicates Work If Mate Pair Information Is Not 'Fixed'?
duplicates picard markduplicates bam written 4.7 years ago by ian.streeter • 10 • updated 23 days ago by Biostar ♦♦ 20
0
votes
1
answer
703
views
1
answer
fetch fully unaligned pairs and pairs with one unaligned read with samtools view
bam samtools written 2.8 years ago by 14134125465346445 • 3.2k • updated 24 days ago by Biostar ♦♦ 20
0
votes
0
answers
80
views
0
answers
Read metadata from a pacbio bam file
R bam pacbio rsamtools sam written 25 days ago by cristian • 50
5
votes
1
answer
161
views
1
answer
Can I open a BAM file without a header in Rsamtools?
bam samtools rsamtools scanbam sequencing written 28 days ago by cristian • 50
0
votes
0
answers
61
views
0
answers
breakseq2 non human data
indel structural variants bam written 28 days ago by guillaume.rbt • 280
0
votes
2
answers
102
views
2
answers
Tool for BAM coverage without the soft clipping base
softclipping bam coverage written 29 days ago by nayshool • 20 • updated 29 days ago by Pierre Lindenbaum ♦ 95k
0
votes
1
answer
92
views
1
answer
BAM file statics and heterozygoty rate
alignment bam written 29 days ago by kk.mahsa • 40 • updated 29 days ago by Gabriel R. • 1.9k
0
votes
2
answers
145
views
5 follow
2
answers
Question about best way to extraction mates of reads
next-gen alignment bam sequencing written 4 weeks ago by user191006 • 10
1
vote
0
answers
113
views
0
answers
CNV Calling- CopywriteR
copywriter bam rstudio written 4 weeks ago by julia • 0 • updated 4 weeks ago by WouterDeCoster ♦ 19k
2
votes
1
answer
147
views
1
answer
From bam paired files to fasta
fasta fastq protein-coding genes paired-reads bam written 4 weeks ago by chevivien • 50 • updated 4 weeks ago by Istvan Albert ♦♦ 71k
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