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<prev • 68 results • page 1 of 3 • next >
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How to ignore truncation error with PySam?
python sam alignment mapping pysam written 4 days ago by O.rka • 60 • updated 1 day ago by Biostar ♦♦ 20
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76
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appropriate way to use pysam.depth
python pysam written 18 days ago by Medhat ♦ 7.9k
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2
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1.8k
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2
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Problem iterating through BAM file using pysam
python sam bam forloop pysam written 2.7 years ago by c9r1y • 0 • updated 5 weeks ago by RamRS ♦ 18k
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3
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5.1k
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3
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cannot import pysam. Module has no attribute error
samtools api python pysam written 3.3 years ago by QVINTVS_FABIVS_MAXIMVS • 2.1k • updated 6 weeks ago by RamRS ♦ 18k
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997
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pysam truncated file error
python samtools pysam written 16 months ago by pupatel • 0 • updated 8 weeks ago by Biostar ♦♦ 20
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2
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261
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2
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Get all the nucleotides from a bam file that is aligning to specific position in the genome
genome samtools alignment position pysam written 12 weeks ago by rsafavi • 40
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1
answer
292
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1
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pysam pileup: what reads appear in the pileup?
software genome alignment pysam sequencing written 3 months ago by aostern • 30
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1
answer
158
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1
answer
pysam: Use read ID to access location
python pysam bam file written 4 months ago by bd2810 • 0
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2
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615
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2
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How to count the total aligned bases in BAM?
python bam pysam pybedtools written 4 months ago by vw • 10
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285
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How to compute target aligned reads/total aligned reads (read enrichment) with Python?
bed bam pybedtools pysam written 4 months ago by vw • 10
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1
answer
285
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5 follow
1
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output differents value between samtools depth and pysam
python pysam written 5 months ago by electronsource75 • 10 • updated 5 months ago by Devon Ryan ♦ 85k
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1
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1.7k
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7 follow
1
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python script error: ImportError: No module named pysam
.py overlapsignature pysam pythonscript written 5 months ago by jaqx008 • 40 • updated 5 months ago by Carlos Borroto • 1.8k
3
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1
answer
413
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1
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calculate fragments depth with pysam
genome python samtools pysam written 5 months ago by electronsource75 • 10
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2
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800
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2
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Pysam fetch for records not exists in VCF files
pysam fetch written 2.0 years ago by always_learning • 930 • updated 5 months ago by Vasisht • 150
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1
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588
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1
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iterate over reads in .SAM file with pysam - IndexError: list index out of range
python pysam sam written 6 months ago by Florian BERNARD • 20 • updated 6 months ago by Pierre Lindenbaum ♦ 113k
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2
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797
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5 follow
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How to use pysam to execute "samtools fastq xxx.sam>xxx.fastq"
samtools pysam written 7 months ago by Zhixue • 10
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219
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Estimate Fragment Size from Single End ChipSeq with (pysam, htseq lib or deeptools API)
htseq deeptools pysam written 8 months ago by ZheFrench • 140
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3
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2.1k
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3
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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 2.4 years ago by kirannbishwa01 • 860 • updated 9 months ago by Matt Shirley ♦ 8.6k
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804
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Pysam read reference positions and sequence do not match
samtools pysam pileup tview written 12 months ago by rlorigro • 0 • updated 11 months ago by Biostar ♦♦ 20
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626
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Create small BAM file with pysam and iterate over reads
samtool bam pysam written 12 months ago by lebedana21 • 0
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1
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458
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1
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Error in pysam: trying to read BAM file using CYTHON
next-gen alignment pysam written 12 months ago by ammarsabir15 • 50 • updated 12 months ago by Devon Ryan ♦ 85k
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1
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560
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1
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pysam not plotting exact values for coverage
alignment pysam coverage written 13 months ago by ammarsabir15 • 50 • updated 13 months ago by Devon Ryan ♦ 85k
1
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0
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706
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Error during htseq-count
htseq-count star pysam written 13 months ago by baffiak1902 • 10
6
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1
answer
2.3k
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1
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pysam: filtering reads based on flag
python samtools pysam hts written 3.3 years ago by QVINTVS_FABIVS_MAXIMVS • 2.1k • updated 15 months ago by Biostar ♦♦ 20
2
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1
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444
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1
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Extract R2F1 reads
samtools pysam structural variation written 15 months ago by IP • 430
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2
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710
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2
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Pysam changes bam format when printing
pysam written 16 months ago by grant.hovhannisyan • 1.1k • updated 16 months ago by i.sudbery • 2.6k
2
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1
answer
725
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1
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Add color tag to bam alignedReads using pysam
pysam rna-seq igv written 17 months ago by pyKey • 30
37
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4
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5.8k
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4
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Tool: pybam - 100% python BAM reader
htspython python bam pysam tool written 2.5 years ago by John ♦ 12k
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1.0k
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Pysam - Different amount of mapped and aligned reads
python alignment pysam mapped written 19 months ago by AlchemistMoz • 20
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1
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1.7k
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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 19 months ago by AlchemistMoz • 20 • updated 19 months ago by Tom_L • 290
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