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<prev • 516 results • page 1 of 18 • next >
3
votes
0
answers
126
views
5 follow
0
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How to calculate percent identity from sam file?
assembly sam samtools mapping cigar written 2 days ago by O.rka • 80
0
votes
0
answers
71
views
0
answers
Read counts at specific locations in SAM files
sam rna-seq hisat2 written 13 days ago by fogarty.mc • 0
3
votes
2
answers
214
views
2
answers
Finding the number of aligned nucleotides per read in a sam file
cigar stings sam written 5 months ago by ioannis • 30 • updated 16 days ago by jilguero888 • 10
1
vote
1
answer
111
views
1
answer
Subsampling aligned SAM/BAM files for RNA-seq analysis
downsampling bam sam rna-seq subsampling written 19 days ago by mohammedtoufiq91 • 30 • updated 19 days ago by WouterDeCoster ♦ 37k
6
votes
5
answers
4.5k
views
7 follow
5
answers
Collect Read Pairs Where At Least One Read Is Mapped
paired-end samtools sam written 5.7 years ago by fridhackery • 140 • updated 5 weeks ago by ying.kev • 0
1
vote
0
answers
147
views
0
answers
Sub-sampling RNA-seq data
fastq bam sam rna-seq downsampling written 5 weeks ago by mohammedtoufiq91 • 30
0
votes
0
answers
114
views
0
answers
Extract reads based on pair orientation
paired end read pair sam bam orientation written 6 weeks ago by Emilie • 0
8
votes
1
answer
4.1k
views
1
answer
How To Force 'Bwa Samse' To Output Multiple Hits In .Sam Format?
sam bwa written 6.8 years ago by Leonor Palmeira ♦ 3.7k • updated 6 weeks ago by Biostar ♦♦ 20
7
votes
1
answer
331
views
1
answer
Is there a way to do read filtering (MAPQ> certain value) on a BAM instead of SAM file?
quality bam sam filtering mapq written 3 months ago by msimmer92 • 150
8
votes
3
answers
242
views
6 follow
3
answers
Find bams with identical names and merge them
shell picard samtools sam bam written 10 weeks ago by brendes • 20 • updated 10 weeks ago by cpad0112 ♦ 11k
7
votes
1
answer
184
views
1
answer
Best way of Merging Multiple Lanes generated by HiSeq 2000, index BAM or VCF?
wgs sam mapping illumina hiseq written 10 weeks ago by venuraherath • 20
5
votes
1
answer
256
views
1
answer
Number of unmapped reads after filtering issue
samtools sam sequencing written 11 weeks ago by max_19 • 30 • updated 11 weeks ago by finswimmer ♦ 11k
2
votes
1
answer
147
views
1
answer
Ignore SAM header section using awk
bam sam sequencing written 11 weeks ago by max_19 • 30 • updated 11 weeks ago by RamRS ♦ 20k
10
votes
3
answers
1.2k
views
5 follow
3
answers
Faster way to get coverage per base
alignment sam written 24 months ago by finswimmer ♦ 11k
6
votes
3
answers
2.6k
views
8 follow
3
answers
Mismatch and Indel statistics from BAM/SAM file
indel bam sam written 22 months ago by sbdk82 • 40 • updated 3 months ago by FatihSarigol • 120
20
votes
1
answer
927
views
5 follow
1
answer
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
bam sam sort markduplicates bqsr tool written 5 months ago by Charlotte.Herzeel • 130
4
votes
1
answer
219
views
1
answer
Contig name in SAM file
contig contigs sam contig name written 3 months ago by maryam.95 • 10 • updated 3 months ago by WouterDeCoster ♦ 37k
5
votes
1
answer
1.3k
views
1
answer
Extracting tlen From BAM File Using htsjdk
htsjdk bam samtools sam tlen written 2.4 years ago by Hakan.Erol.HE • 10 • updated 3 months ago by Biostar ♦♦ 20
2
votes
2
answers
216
views
2
answers
Making BAM or SAM files equivalent
alignment popoolation2 sam popoolation bam written 3 months ago by keturner123 • 0 • updated 3 months ago by finswimmer ♦ 11k
2
votes
1
answer
173
views
1
answer
Filtering noise out of SAM file using CIGAR
cigar sam written 3 months ago by blur • 90 • updated 3 months ago by Carambakaracho • 930
0
votes
1
answer
184
views
1
answer
Errors with samtools depth on merged bam file
bam samtools sam written 4 months ago by rbronste • 230 • updated 4 months ago by bioExplorer ♦ 3.7k
0
votes
0
answers
176
views
0
answers
Filtering SAM file based on column numbers
filter alignment sam written 4 months ago by elena.syp • 0 • updated 4 months ago by Pierre Lindenbaum ♦ 118k
5
votes
1
answer
367
views
1
answer
sam file not showing multi mapped reads
bowtie2 sam written 6 months ago by Moses • 60 • updated 4 months ago by Biostar ♦♦ 20
1
vote
1
answer
246
views
1
answer
Get genes and coverage/depth per gene from sam/bam
ngs bam sam coverage per gene depth per gene written 4 months ago by prishly • 0 • updated 4 months ago by Charles Warden ♦ 6.4k
1
vote
1
answer
304
views
1
answer
Why does bowtie2 Terminate with: Saw ASCII character 10 but expected 33-based Phred qual....?
bowtie2 sam mapping signleread written 5 months ago by jaqx008 • 40 • updated 5 months ago by Istvan Albert ♦♦ 79k
0
votes
0
answers
246
views
0
answers
How to ignore truncation error with PySam?
python sam alignment mapping pysam written 5 months ago by O.rka • 80 • updated 5 months ago by Biostar ♦♦ 20
5
votes
1
answer
318
views
1
answer
A constant problem with SAM file header
software error bowtie2 sam written 5 months ago by popescuiofelia • 10 • updated 5 months ago by h.mon ♦ 24k
0
votes
1
answer
545
views
1
answer
How to extract sequence message from SAM?
bed sam sequencing written 22 months ago by Jeason Rad • 30 • updated 5 months ago by Biostar ♦♦ 20
3
votes
1
answer
434
views
8 follow
1
answer
Merge multiple Sam files to one big Sam file. How?
overlapzscore samtools sam heatmap written 5 months ago by jaqx008 • 40 • updated 5 months ago by gocougs • 20
4
votes
1
answer
263
views
1
answer
Position of aligned read in SAM file.
sam bwa written 5 months ago by relinquisheddragon • 0
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