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Showing: pysam • reset
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6
votes
1
answer
1.4k
views
1
answer
pysam: filtering reads based on flag
python samtools pysam hts written 2.1 years ago by QVINTVS_FABIVS_MAXIMVS • 1.9k • updated 4 weeks ago by Biostar ♦♦ 20
2
votes
1
answer
181
views
1
answer
Extract R2F1 reads
samtools pysam structural variation written 6 weeks ago by Iñigo Prada • 350
1
vote
0
answers
163
views
0
answers
pysam truncated file error
python samtools pysam written 7 weeks ago by pupatel • 0
11
votes
2
answers
171
views
2
answers
Pysam changes bam format when printing
pysam written 9 weeks ago by grant.hovhannisyan • 120 • updated 9 weeks ago by i.sudbery • 1.4k
2
votes
1
answer
202
views
1
answer
Add color tag to bam alignedReads using pysam
pysam rna-seq igv written 3 months ago by pyKey • 10
26
votes
4
answers
2.8k
views
4
answers
Tool: pybam - 100% python BAM reader
htspython python bam pysam tool written 16 months ago by John ♦ 11k
0
votes
0
answers
291
views
0
answers
Pysam - Different amount of mapped and aligned reads
python alignment pysam mapped written 5 months ago by AlchemistMoz • 10
3
votes
1
answer
350
views
1
answer
How to filter/view reads mapped to multiple locations using samtools or pysam
python samtools pysam written 5 months ago by AlchemistMoz • 10 • updated 5 months ago by Tom_L • 190
2
votes
1
answer
186
views
1
answer
Necessary to close pysam.AlignmentFile?
python bam pysam written 5 months ago by AlchemistMoz • 10 • updated 5 months ago by Devon Ryan ♦ 70k
0
votes
0
answers
262
views
0
answers
What does the reference_id = -1 indicate in a .sam file read with pysam?
python miseq pysam bowtie sam-file written 6 months ago by osman.christof • 0
5
votes
2
answers
349
views
2
answers
Pysam Fetching specified regions
python pysam written 6 months ago by AlchemistMoz • 10
3
votes
1
answer
394
views
1
answer
Need help interpreting gdb backtrace from a SAMtools segmentation fault (or help editing SAM/BAM files!)
bam samtools pysam written 8 months ago by russianconcussion • 10
0
votes
1
answer
466
views
1
answer
Filter low quality reads in bam files
python next-gen pysam written 8 months ago by ammarsabir15 • 50 • updated 8 months ago by Brian Bushnell ♦ 13k
2
votes
1
answer
357
views
1
answer
Error Filtering BAM file based on mapping qualities in python's pysam
next-gen alignment pysam written 8 months ago by ammarsabir15 • 50 • updated 8 months ago by John ♦ 11k
0
votes
1
answer
296
views
1
answer
For loop that continues finding matches in a file
python loop fastq pysam written 8 months ago by yarmda • 0 • updated 8 months ago by WouterDeCoster ♦ 20k
1
vote
1
answer
341
views
1
answer
pysam fetch with partial reference name
pysam python fetch bamfile substring written 9 months ago by yarmda • 0 • updated 9 months ago by Devon Ryan ♦ 70k
2
votes
1
answer
350
views
1
answer
Pysam fetch for records not exists in VCF files
pysam fetch written 10 months ago by always_learning • 780
3
votes
0
answers
389
views
0
answers
Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
samtools pysam mpileup written 10 months ago by abascalfederico • 960
1
vote
0
answers
332
views
0
answers
Entire Sequence from Bam File using Python Pysam Module
python ngs alignment pysam written 11 months ago by Saudi Bioinformatician • 20
4
votes
2
answers
979
views
2
answers
Pysam under pypy?
python pysam pypy written 2.5 years ago by John ♦ 11k • updated 11 months ago by Eric T. • 1.8k
4
votes
0
answers
492
views
0
answers
Using pysam to parse bamfile and fetch based on bedfile, looking to speed up code.
python pysam written 12 months ago by Daniel • 3.4k
3
votes
2
answers
660
views
2
answers
Problems with Pysam and deeptools [Help me, please..]
deeptools pysam written 13 months ago by mink2mink2 • 0
1
vote
1
answer
396
views
1
answer
let me know examples of "pysam.view()" for counting BAM.
samtools view pysam written 13 months ago by mink2mink2 • 0 • updated 13 months ago by pld ♦ 4.6k
15
votes
2
answers
950
views
2
answers
Pysam is giving - ValueError: reference_id -1 out of range 0<=tid<65334. Any suggestions?
sam bam pysam reference_id written 14 months ago by kirannbishwa01 • 500
6
votes
1
answer
466
views
1
answer
Reads in BAM file overlapping coordinates
reads bam pysam snp written 15 months ago by madhavkurup1991 • 0 • updated 15 months ago by Jorge Amigo ♦ 9.8k
4
votes
0
answers
443
views
0
answers
Pysam: Determine intra-read-position of Base at Pileupsite
bseq pysam bam sam written 15 months ago by thm_junk • 0
3
votes
2
answers
1.0k
views
2
answers
Pysam (python) problem parsing BAM reference id
python bam sam pysam written 16 months ago by liorglic • 10 • updated 16 months ago by Matt Shirley ♦ 7.7k
0
votes
1
answer
935
views
1
answer
Mate pair positions using pysam
python mate pair pysam written 2.0 years ago by QVINTVS_FABIVS_MAXIMVS • 1.9k • updated 17 months ago by horticulturesh • 0
2
votes
1
answer
782
views
1
answer
obtaining a pileup with read names from a bam alignment
alignment next-gen samtools pysam mpileup written 17 months ago by bernardo1963 • 10 • updated 17 months ago by Devon Ryan ♦ 70k
2
votes
2
answers
969
views
2
answers
Problem iterating through BAM file using pysam
python sam bam forloop pysam written 18 months ago by c9r1y • 0 • updated 18 months ago by Matt Shirley ♦ 7.7k
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