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<prev • 49 results • page 1 of 2 • next >
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pysam truncated file error
python samtools pysam written 1 day ago by pupatel • 0
11
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2
answers
118
views
2
answers
Pysam changes bam format when printing
pysam written 13 days ago by grant.hovhannisyan • 20 • updated 13 days ago by i.sudbery • 1.3k
2
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1
answer
151
views
1
answer
Add color tag to bam alignedReads using pysam
pysam rna-seq igv written 7 weeks ago by pyKey • 10
26
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4
answers
2.5k
views
4
answers
Tool: pybam - 100% python BAM reader
htspython python bam pysam tool written 14 months ago by John ♦ 11k
0
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0
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223
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Pysam - Different amount of mapped and aligned reads
python alignment pysam mapped written 3 months ago by AlchemistMoz • 10
3
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1
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264
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1
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How to filter/view reads mapped to multiple locations using samtools or pysam
python samtools pysam written 3 months ago by AlchemistMoz • 10 • updated 3 months ago by Tom_L • 180
2
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1
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153
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1
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Necessary to close pysam.AlignmentFile?
python bam pysam 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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222
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What does the reference_id = -1 indicate in a .sam file read with pysam?
python miseq pysam bowtie sam-file written 4 months ago by osman.christof • 0
5
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2
answers
270
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2
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Pysam Fetching specified regions
python pysam written 4 months ago by AlchemistMoz • 10
3
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1
answer
347
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1
answer
Need help interpreting gdb backtrace from a SAMtools segmentation fault (or help editing SAM/BAM files!)
bam samtools pysam written 6 months ago by russianconcussion • 10
0
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1
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379
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1
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Filter low quality reads in bam files
python next-gen pysam written 6 months ago by ammarsabir15 • 40 • updated 6 months ago by Brian Bushnell ♦ 12k
2
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1
answer
311
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1
answer
Error Filtering BAM file based on mapping qualities in python's pysam
next-gen alignment pysam written 6 months ago by ammarsabir15 • 40 • updated 6 months ago by John ♦ 11k
0
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1
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268
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1
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For loop that continues finding matches in a file
python loop fastq pysam written 6 months ago by yarmda • 0 • updated 6 months ago by WouterDeCoster ♦ 19k
1
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1
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293
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1
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pysam fetch with partial reference name
pysam python fetch bamfile substring written 7 months ago by yarmda • 0 • updated 7 months ago by Devon Ryan ♦ 68k
2
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1
answer
314
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1
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Pysam fetch for records not exists in VCF files
pysam fetch written 8 months ago by always_learning • 780
3
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0
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336
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0
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Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
samtools pysam mpileup written 8 months ago by abascalfederico • 930
1
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0
answers
287
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0
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Entire Sequence from Bam File using Python Pysam Module
python ngs alignment pysam written 9 months ago by Saudi Bioinformatician • 20
4
votes
2
answers
934
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2
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Pysam under pypy?
python pysam pypy written 2.3 years ago by John ♦ 11k • updated 10 months ago by Eric T. • 1.7k
4
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0
answers
426
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0
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Using pysam to parse bamfile and fetch based on bedfile, looking to speed up code.
python pysam written 11 months ago by Daniel • 3.4k
3
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2
answers
578
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2
answers
Problems with Pysam and deeptools [Help me, please..]
deeptools pysam written 11 months ago by mink2mink2 • 0
1
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1
answer
347
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1
answer
let me know examples of "pysam.view()" for counting BAM.
samtools view pysam written 11 months ago by mink2mink2 • 0 • updated 11 months ago by pld ♦ 4.5k
14
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2
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875
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2
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Pysam is giving - ValueError: reference_id -1 out of range 0<=tid<65334. Any suggestions?
sam bam pysam reference_id written 13 months ago by kirannbishwa01 • 460
6
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1
answer
431
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1
answer
Reads in BAM file overlapping coordinates
reads bam pysam snp written 13 months ago by madhavkurup1991 • 0 • updated 13 months ago by Jorge Amigo ♦ 9.7k
4
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0
answers
401
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0
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Pysam: Determine intra-read-position of Base at Pileupsite
bseq pysam bam sam written 13 months ago by thm_junk • 0
3
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2
answers
926
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2
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Pysam (python) problem parsing BAM reference id
python bam sam pysam written 14 months ago by liorglic • 10 • updated 14 months ago by Matt Shirley ♦ 7.3k
0
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1
answer
892
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1
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Mate pair positions using pysam
python mate pair pysam written 23 months ago by QVINTVS_FABIVS_MAXIMVS • 1.9k • updated 15 months ago by horticulturesh • 0
2
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1
answer
718
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1
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obtaining a pileup with read names from a bam alignment
alignment next-gen samtools pysam mpileup written 16 months ago by bernardo1963 • 10 • updated 16 months ago by Devon Ryan ♦ 68k
2
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2
answers
868
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2
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Problem iterating through BAM file using pysam
python sam bam forloop pysam written 16 months ago by c9r1y • 0 • updated 16 months ago by Matt Shirley ♦ 7.3k
5
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0
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554
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0
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Truncating BAM Files
bam samtools sam rna-seq pysam written 19 months ago by JameB11 • 0 • updated 17 months ago by Biostar ♦♦ 20
3
votes
1
answer
577
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1
answer
How to cache reads?
genome alignment sequence samtools pysam written 17 months ago by everrove • 0 • updated 17 months ago by Manuel Landesfeind • 1.1k
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