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Showing: pysam • reset
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<prev • 58 results • page 1 of 2 • next >
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iterate over reads in .SAM file with pysam - IndexError: list index out of range
python pysam sam written 25 days ago by Florian BERNARD • 20 • updated 25 days ago by Pierre Lindenbaum ♦ 106k
5
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2
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444
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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 weeks ago by Zhixue • 0
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0
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105
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0
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Estimate Fragment Size from Single End ChipSeq with (pysam, htseq lib or deeptools API)
htseq deeptools pysam written 12 weeks ago by ZheFrench • 120
15
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3
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1.6k
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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 22 months ago by kirannbishwa01 • 770 • updated 3 months ago by Matt Shirley ♦ 8.3k
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390
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Pysam read reference positions and sequence do not match
samtools pysam pileup tview written 6 months ago by rlorigro • 0 • updated 5 months ago by Biostar ♦♦ 20
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380
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Create small BAM file with pysam and iterate over reads
samtool bam pysam written 5 months ago by lebedana21 • 0
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1
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291
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1
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Error in pysam: trying to read BAM file using CYTHON
next-gen alignment pysam written 6 months ago by ammarsabir15 • 50 • updated 6 months ago by Devon Ryan ♦ 78k
0
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1
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366
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1
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pysam not plotting exact values for coverage
alignment pysam coverage written 7 months ago by ammarsabir15 • 50 • updated 7 months ago by Devon Ryan ♦ 78k
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436
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Error during htseq-count
htseq-count star pysam written 7 months ago by baffiak1902 • 10
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1
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1.8k
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1
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pysam: filtering reads based on flag
python samtools pysam hts written 2.8 years ago by QVINTVS_FABIVS_MAXIMVS • 2.0k • updated 9 months ago by Biostar ♦♦ 20
2
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1
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335
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1
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Extract R2F1 reads
samtools pysam structural variation written 9 months ago by IP • 350
1
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0
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555
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0
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pysam truncated file error
python samtools pysam written 9 months ago by pupatel • 0
11
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2
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425
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2
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Pysam changes bam format when printing
pysam written 10 months ago by grant.hovhannisyan • 730 • updated 10 months ago by i.sudbery • 1.9k
2
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1
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475
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1
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Add color tag to bam alignedReads using pysam
pysam rna-seq igv written 11 months ago by pyKey • 20
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4
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4.3k
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4
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Tool: pybam - 100% python BAM reader
htspython python bam pysam tool written 2.0 years ago by John ♦ 12k
0
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0
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614
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0
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Pysam - Different amount of mapped and aligned reads
python alignment pysam mapped written 13 months ago by AlchemistMoz • 20
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1
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960
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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 13 months ago by AlchemistMoz • 20 • updated 13 months ago by Tom_L • 260
2
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1
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338
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1
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Necessary to close pysam.AlignmentFile?
python bam pysam written 14 months ago by AlchemistMoz • 20 • updated 14 months ago by Devon Ryan ♦ 78k
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0
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601
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0
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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 14 months ago by osman.christof • 0
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2
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914
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2
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Pysam Fetching specified regions
python pysam written 14 months ago by AlchemistMoz • 20
3
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1
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632
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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 16 months ago by russianconcussion • 20
0
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1
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921
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1
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Filter low quality reads in bam files
python next-gen pysam written 16 months ago by ammarsabir15 • 50 • updated 16 months ago by Brian Bushnell ♦ 15k
2
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1
answer
616
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1
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Error Filtering BAM file based on mapping qualities in python's pysam
next-gen alignment pysam written 16 months ago by ammarsabir15 • 50 • updated 16 months ago by John ♦ 12k
0
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1
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439
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1
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For loop that continues finding matches in a file
python loop fastq pysam written 16 months ago by yarmda • 0 • updated 16 months ago by WouterDeCoster ♦ 27k
1
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1
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687
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1
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pysam fetch with partial reference name
pysam python fetch bamfile substring written 17 months ago by yarmda • 0 • updated 17 months ago by Devon Ryan ♦ 78k
2
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1
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567
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1
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Pysam fetch for records not exists in VCF files
pysam fetch written 18 months ago by always_learning • 870
3
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0
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631
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0
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Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
samtools pysam mpileup written 18 months ago by abascalfederico • 1.0k
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0
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580
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Entire Sequence from Bam File using Python Pysam Module
python ngs alignment pysam written 19 months ago by Saudi Bioinformatician • 30
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2
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1.2k
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2
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Pysam under pypy?
python pysam pypy written 3.2 years ago by John ♦ 12k • updated 20 months ago by Eric T. • 2.1k
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914
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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 20 months ago by Daniel • 3.5k
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