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105
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From sam data, how do I tell from which fastq file each read came from?
bowtie2 sam read file origin parsing written 1 day ago by bitjunkie • 40
5
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3
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141
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7 follow
3
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How to find the mapping quality (mapQ) score of a variant
vcf sam written 2 days ago by gmora • 10 • updated 1 day ago by Lauren M. • 10
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2
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12k
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2
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BAM/SAM to FASTA conversion
bam sam written 2.5 years ago by biolab • 890 • updated 11 days ago by Chadi Saad • 30
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104
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Blast+ Sam outfmt parameter check
sam blast written 13 days ago by larvalanobium • 0
3
votes
1
answer
215
views
1
answer
Increase the fifth column ( MAPQ) value in Sam file
mapq alignment sam sequencing written 4 weeks ago by madhu.9124 • 10 • updated 4 weeks ago by novice • 670
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195
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Paired-read alignment length from BAM/SAM file
paired-read alignment sam bam written 5 weeks ago by Soumitra Pal • 10
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1
answer
148
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1
answer
Difference between chimeric alignments and multiple mapping
sam flag alignment samtools sam sequencing written 5 weeks ago by Vanilla • 30 • updated 5 weeks ago by Devon Ryan ♦ 68k
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2
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2.9k
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2
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Cigar And Sequence Length Are Inconsistent In Sam File
sam written 4.2 years ago by xiaoyanli82 • 0 • updated 6 weeks ago by Biostar ♦♦ 20
0
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109
views
0
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Read metadata from a pacbio bam file
R bam pacbio rsamtools sam written 7 weeks ago by cristian • 50
3
votes
0
answers
687
views
0
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direct two-color Agilent SAM analysis?
agilent R sam microarray written 2.2 years ago by evansjo • 10 • updated 7 weeks ago by Ace • 0
4
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2
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253
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5 follow
2
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How to extract reads with no INDEL?
indel samtools sam written 9 weeks ago by Jeason Rad • 30 • updated 9 weeks ago by dariober • 7.9k
0
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1
answer
172
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1
answer
Mismatch and Indel statistics from BAM/SAM file
indel bam sam written 10 weeks ago by sbdk82 • 30 • updated 10 weeks ago by Brian Bushnell ♦ 13k
0
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1
answer
162
views
1
answer
How to extract sequence message from SAM?
bed sam sequencing written 11 weeks ago by Jeason Rad • 30 • updated 11 weeks ago by Pierre Lindenbaum ♦ 96k
4
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2
answers
185
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2
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Extract specific fragments from SAM and count them
sam snp written 11 weeks ago by Jeason Rad • 30 • updated 11 weeks ago by kennethcondon2007 • 810
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1
answer
134
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1
answer
Parsing reads from SAM file by Fwd-Fwd orientation
flag R sam written 12 weeks ago by ThePresident • 40 • updated 12 weeks ago by Pierre Lindenbaum ♦ 96k
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0
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183
views
0
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How to extract only continuously aligned reads from a SAMfile
alignment samtools sam written 3 months ago by yarmda • 0
1
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2
answers
160
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2
answers
samtools updation in linux
next-gen sam written 3 months ago by shafnaasmy.v.s • 0 • updated 3 months ago by WouterDeCoster ♦ 20k
0
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0
answers
158
views
0
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What are the various procedures involved in DNA Mapping ?
genome java sequencing fastq sam written 3 months ago by plabanbiswas96 • 10
8
votes
1
answer
328
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1
answer
Getting edit distance from sam tags MD & NM: conceptual misunderstanding?
edit distance sam written 3 months ago by WouterDeCoster ♦ 20k • updated 3 months ago by Santosh Anand • 2.7k
2
votes
1
answer
203
views
1
answer
Understanding Picards HsMetrics
picardtools bam sam written 3 months ago by finswimmer • 300 • updated 3 months ago by Pierre Lindenbaum ♦ 96k
0
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0
answers
122
views
0
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Bam file without any sequence
psl2sam sam blat written 3 months ago by tiago211287 • 720
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1
answer
158
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1
answer
Questions about LB field in SAM specification for PCR duplicate removal
sam markduplicates written 3 months ago by James Ashmore • 1.7k
0
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1
answer
208
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1
answer
Number of reference sequence contigs in sam/bam header does not match the number in my fasta
fasta bowtie2 contig sam bam written 4 months ago by marcusanaymik • 10 • updated 4 months ago by Brian Bushnell ♦ 13k
5
votes
2
answers
248
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5 follow
2
answers
Faster way to get coverage per base
alignment sam written 4 months ago by finswimmer • 300 • updated 4 months ago by Vivek Todur • 30
13
votes
0
answers
268
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5 follow
0
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Error of bam-to-sam conversion using samtools
tophat2 samtools sam rna-seq bam written 4 months ago by Gary • 380 • updated 4 months ago by genomax ♦ 30k
0
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1
answer
329
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1
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Extract the mapped contig sequences from SAM/BAM file
bam samtools sam bwa written 4 months ago by sbdk82 • 30 • updated 4 months ago by haro • 120
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0
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150
views
0
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Most represented reads in SAM file
reads sam representated written 4 months ago by Picasa • 290
3
votes
1
answer
179
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1
answer
SAM files alignment section: PNEXT
bam samtools sam written 4 months ago by AlchemistMoz • 10 • updated 4 months ago by Devon Ryan ♦ 68k
0
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0
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194
views
0
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Novoalign: right index? and SAM output
novoalign ngs sam mapping written 4 months ago by maude • 0 • updated 4 months ago by Devon Ryan ♦ 68k
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189
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0
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How to extract all - strand mapped reads location of reference genome using BAM file?
reads ngs bam sam written 4 months ago by BioGeek • 80
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