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<prev • 511 results • page 1 of 18 • next >
7
votes
1
answer
208
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 8 weeks ago by msimmer92 • 50
8
votes
3
answers
176
views
7 follow
3
answers
Find bams with identical names and merge them
shell picard samtools sam bam written 18 days ago by brendes • 20 • updated 17 days ago by cpad0112 ♦ 10k
7
votes
1
answer
118
views
1
answer
Best way of Merging Multiple Lanes generated by HiSeq 2000, index BAM or VCF?
wgs sam mapping illumina hiseq written 18 days ago by venuraherath • 20
5
votes
1
answer
191
views
1
answer
Number of unmapped reads after filtering issue
samtools sam sequencing written 25 days ago by max_19 • 10 • updated 24 days ago by finswimmer ♦ 9.0k
2
votes
1
answer
105
views
1
answer
Ignore SAM header section using awk
bam sam sequencing written 25 days ago by max_19 • 10 • updated 25 days ago by RamRS ♦ 20k
9
votes
3
answers
1.0k
views
5 follow
3
answers
Faster way to get coverage per base
alignment sam written 22 months ago by finswimmer ♦ 9.0k
6
votes
3
answers
2.3k
views
8 follow
3
answers
Mismatch and Indel statistics from BAM/SAM file
indel bam sam written 20 months ago by sbdk82 • 40 • updated 5 weeks ago by FatihSarigol • 110
19
votes
1
answer
757
views
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 3 months ago by Charlotte.Herzeel • 130
4
votes
1
answer
171
views
1
answer
Contig name in SAM file
contig contigs sam contig name written 6 weeks ago by maryam.95 • 10 • updated 6 weeks ago by WouterDeCoster ♦ 36k
5
votes
1
answer
1.3k
views
1
answer
Extracting tlen From BAM File Using htsjdk
htsjdk bam samtools sam tlen written 2.3 years ago by Hakan.Erol.HE • 10 • updated 7 weeks ago by Biostar ♦♦ 20
2
votes
2
answers
179
views
2
answers
Making BAM or SAM files equivalent
alignment popoolation2 sam popoolation bam written 7 weeks ago by keturner123 • 0 • updated 7 weeks ago by finswimmer ♦ 9.0k
2
votes
1
answer
131
views
1
answer
Filtering noise out of SAM file using CIGAR
cigar sam written 8 weeks ago by blur • 90 • updated 8 weeks ago by Carambakaracho • 670
0
votes
1
answer
143
views
1
answer
Errors with samtools depth on merged bam file
bam samtools sam written 9 weeks ago by rbronste • 230 • updated 9 weeks ago by Vijay Lakhujani ♦ 3.5k
0
votes
0
answers
132
views
0
answers
Filtering SAM file based on column numbers
filter alignment sam written 11 weeks ago by elena.syp • 0 • updated 11 weeks ago by Pierre Lindenbaum ♦ 116k
2
votes
1
answer
271
views
1
answer
sam file not showing multi mapped reads
bowtie2 sam written 4 months ago by mossigstamboulian • 30 • updated 11 weeks ago by Biostar ♦♦ 20
1
vote
1
answer
192
views
1
answer
Get genes and coverage/depth per gene from sam/bam
ngs bam sam coverage per gene depth per gene written 11 weeks ago by prishly • 0 • updated 11 weeks ago by Charles Warden ♦ 5.9k
1
vote
1
answer
203
views
1
answer
Why does bowtie2 Terminate with: Saw ASCII character 10 but expected 33-based Phred qual....?
bowtie2 sam mapping signleread written 3 months ago by jaqx008 • 40 • updated 3 months ago by Istvan Albert ♦♦ 78k
0
votes
0
answers
180
views
0
answers
How to ignore truncation error with PySam?
python sam alignment mapping pysam written 3 months ago by O.rka • 70 • updated 3 months ago by Biostar ♦♦ 20
5
votes
1
answer
236
views
1
answer
A constant problem with SAM file header
software error bowtie2 sam written 3 months ago by popescuiofelia • 0 • updated 3 months ago by h.mon ♦ 22k
3
votes
1
answer
150
views
1
answer
Finding the number of aligned nucleotides per read in a sam file
cigar stings sam written 3 months ago by ioannis • 30 • updated 3 months ago by Pierre Lindenbaum ♦ 116k
0
votes
1
answer
510
views
1
answer
How to extract sequence message from SAM?
bed sam sequencing written 20 months ago by Jeason Rad • 30 • updated 3 months ago by Biostar ♦♦ 20
3
votes
1
answer
269
views
8 follow
1
answer
Merge multiple Sam files to one big Sam file. How?
overlapzscore samtools sam heatmap written 3 months ago by jaqx008 • 40 • updated 3 months ago by gocougs • 0
4
votes
1
answer
197
views
1
answer
Position of aligned read in SAM file.
sam bwa written 3 months ago by relinquisheddragon • 0
1
vote
1
answer
1.7k
views
1
answer
I can't convert the sam file to fastq file.
fastq sam written 2.9 years ago by porori3000 • 0 • updated 4 months ago by RamRS ♦ 20k
2
votes
1
answer
1.7k
views
1
answer
BLAST geneate Output SAM file , Missing aligned sequences.
blast bam sam output rna-seq written 2.9 years ago by clear.choi • 30 • updated 4 months ago by RamRS ♦ 20k
3
votes
0
answers
778
views
0
answers
softclip vs mismatch at either end
alignment sam written 2.4 years ago by -_- • 730 • updated 4 months ago by Biostar ♦♦ 20
2
votes
2
answers
1.9k
views
2
answers
Problem iterating through BAM file using pysam
python sam bam forloop pysam written 2.9 years ago by c9r1y • 0 • updated 4 months ago by RamRS ♦ 20k
3
votes
1
answer
2.0k
views
1
answer
Extracting Reads by position
alignment sam bam written 2.9 years ago by michael.madans94 • 10 • updated 4 months ago by RamRS ♦ 20k
3
votes
1
answer
321
views
1
answer
Adding optional tags to a BAM file
single-cell bam sam rna-seq awk written 4 months ago by sc243 • 10
0
votes
0
answers
207
views
0
answers
calculating sequencing coverage for metagenome samples
illumina-hi-seq metagenomics sam bowtie2 written 4 months ago by mossigstamboulian • 30
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