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pysam pileup: what reads appear in the pileup?
software genome alignment pysam sequencing written 18 days ago by aostern • 20
1
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1
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88
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1
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pysam: Use read ID to access location
python pysam bam file written 5 weeks ago by bd2810 • 0
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2
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302
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2
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How to count the total aligned bases in BAM?
python bam pysam pybedtools written 7 weeks ago by vw • 10
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188
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How to compute target aligned reads/total aligned reads (read enrichment) with Python?
bed bam pybedtools pysam written 8 weeks ago by vw • 10
3
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1
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158
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5 follow
1
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output differents value between samtools depth and pysam
python pysam written 9 weeks ago by electronsource75 • 10 • updated 8 weeks ago by Devon Ryan ♦ 81k
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594
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7 follow
1
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python script error: ImportError: No module named pysam
.py overlapsignature pysam pythonscript written 9 weeks ago by jaqx008 • 30 • updated 9 weeks ago by Carlos Borroto • 1.7k
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1
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256
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1
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calculate fragments depth with pysam
genome python samtools pysam written 11 weeks ago by electronsource75 • 10
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2
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690
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2
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Pysam fetch for records not exists in VCF files
pysam fetch written 21 months ago by always_learning • 910 • updated 10 weeks ago by Vasisht • 150
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1
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295
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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 3 months ago by Florian BERNARD • 20 • updated 3 months ago by Pierre Lindenbaum ♦ 110k
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2
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609
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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 4 months ago by Zhixue • 0
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149
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Estimate Fragment Size from Single End ChipSeq with (pysam, htseq lib or deeptools API)
htseq deeptools pysam written 5 months ago by ZheFrench • 130
15
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3
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1.9k
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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 2.1 years ago by kirannbishwa01 • 810 • updated 6 months ago by Matt Shirley ♦ 8.4k
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584
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Pysam read reference positions and sequence do not match
samtools pysam pileup tview written 9 months ago by rlorigro • 0 • updated 8 months ago by Biostar ♦♦ 20
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521
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Create small BAM file with pysam and iterate over reads
samtool bam pysam written 9 months ago by lebedana21 • 0
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1
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362
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1
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Error in pysam: trying to read BAM file using CYTHON
next-gen alignment pysam written 9 months ago by ammarsabir15 • 50 • updated 9 months ago by Devon Ryan ♦ 81k
0
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1
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455
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1
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pysam not plotting exact values for coverage
alignment pysam coverage written 10 months ago by ammarsabir15 • 50 • updated 10 months ago by Devon Ryan ♦ 81k
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559
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Error during htseq-count
htseq-count star pysam written 10 months ago by baffiak1902 • 10
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1
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2.1k
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1
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pysam: filtering reads based on flag
python samtools pysam hts written 3.0 years ago by QVINTVS_FABIVS_MAXIMVS • 2.1k • updated 12 months ago by Biostar ♦♦ 20
2
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1
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385
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1
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Extract R2F1 reads
samtools pysam structural variation written 12 months ago by IP • 360
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747
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pysam truncated file error
python samtools pysam written 13 months ago by pupatel • 0
11
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2
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561
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2
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Pysam changes bam format when printing
pysam written 13 months ago by grant.hovhannisyan • 900 • updated 13 months ago by i.sudbery • 2.4k
2
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1
answer
603
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1
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Add color tag to bam alignedReads using pysam
pysam rna-seq igv written 14 months ago by pyKey • 30
35
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4
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5.0k
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4
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Tool: pybam - 100% python BAM reader
htspython python bam pysam tool written 2.3 years ago by John ♦ 12k
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800
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Pysam - Different amount of mapped and aligned reads
python alignment pysam mapped written 16 months ago by AlchemistMoz • 20
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1
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1.3k
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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 16 months ago by AlchemistMoz • 20 • updated 16 months ago by Tom_L • 270
2
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1
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404
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1
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Necessary to close pysam.AlignmentFile?
python bam pysam written 17 months ago by AlchemistMoz • 20 • updated 17 months ago by Devon Ryan ♦ 81k
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711
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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 17 months ago by osman.christof • 0
5
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2
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1.2k
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2
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Pysam Fetching specified regions
python pysam written 17 months ago by AlchemistMoz • 20
3
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1
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722
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1
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Need help interpreting gdb backtrace from a SAMtools segmentation fault (or help editing SAM/BAM files!)
bam samtools pysam written 19 months ago by russianconcussion • 20
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1.1k
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1
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Filter low quality reads in bam files
python next-gen pysam written 19 months ago by ammarsabir15 • 50 • updated 19 months ago by Brian Bushnell ♦ 15k
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