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Import Module error Pysam
pysam snp written 11 days ago by prahalad.atreyaa • 0 • updated 11 days ago by Joe ♦ 14k
0
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1
answer
146
views
1
answer
Pysam not finding mapped reads in BAM file
chip-seq bam samtools pysam written 7 weeks ago by taraeicher • 10
1
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1
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127
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1
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Parsing tabix with pysam
tabix pysam written 8 weeks ago by Alex Reynolds ♦ 28k • updated 8 weeks ago by John Marshall ♦ 1.7k
2
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1
answer
153
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1
answer
Finding all bases at a specific genomic position
pysam pileup written 9 weeks ago by dodani • 0
2
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1
answer
1.1k
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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 2.8 years ago by ammarsabir15 • 60 • updated 12 weeks ago by Biostar ♦♦ 20
5
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1
answer
202
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1
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Infer order of supplementary alignments [pysam]
alignment pysam written 5 months ago by WouterDeCoster ♦ 40k • updated 4 months ago by IP • 590
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362
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Extracting CIGAR string from a specific region of a read in a bam file using pysam?
cigar bam pysam rna-seq written 4 months ago by kiki4133 • 0
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214
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correct mark duplicated error using python and pysam to filter out secondary alignments
python pysam written 5 months ago by bioguy24 • 190
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1
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214
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1
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How to identify RNA-seq reads spanning given genomic range?
python pysam rna-seq written 5 months ago by agicict • 140 • updated 5 months ago by lakhujanivijay ♦ 4.4k
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270
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Pysam: Is there a way to check if there are inserts when looking at read overalps.
alignment pysam written 5 months ago by ahmed.kidwai • 0 • updated 5 months ago by RamRS ♦ 24k
4
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0
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337
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Pysam.view report 'pysam.utils.SamtoolsError: "samtools returned with error 1: stdout=, stderr=samtools view: invalid option -- ' ''
samtools pysam written 6 months ago by SDin • 0 • updated 6 months ago by ATpoint ♦ 23k
3
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1
answer
355
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1
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unmapped reads with pysam
pysam written 7 months ago by grant.hovhannisyan • 1.7k
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304
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Analogy of exifread library in pysam for bam and vcf header files
vcf bam bcftools pysam htslib written 8 months ago by aiteteji • 10
3
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1
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481
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1
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Pysam VariantFile.fetch() without specifying contig
vcf python pysam written 8 months ago by ricardoguerreiro2121 • 20
3
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1
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625
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1
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pysam difference between template_length and reference_length
genome next-gen pysam written 10 months ago by Medhat ♦ 8.4k • updated 10 months ago by Devon Ryan ♦ 91k
0
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386
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0
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pysam: How do I type an AlignedSegment in Cython?
cython pysam written 11 months ago by Click downvote • 670 • updated 11 months ago by Biostar ♦♦ 20
0
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0
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456
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How to ignore truncation error with PySam?
python sam alignment mapping pysam written 11 months ago by O.rka • 120 • updated 11 months ago by Biostar ♦♦ 20
0
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471
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appropriate way to use pysam.depth
python pysam written 11 months ago by Medhat ♦ 8.4k
3
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2
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2.2k
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2
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Problem iterating through BAM file using pysam
python sam bam forloop pysam written 3.6 years ago by c9r1y • 10 • updated 12 months ago by RamRS ♦ 24k
7
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3
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6.2k
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3
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cannot import pysam. Module has no attribute error
samtools api python pysam written 4.2 years ago by QVINTVS_FABIVS_MAXIMVS • 2.3k • updated 12 months ago by RamRS ♦ 24k
1
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1.7k
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pysam truncated file error
python samtools pysam written 2.2 years ago by pupatel • 0 • updated 13 months ago by Biostar ♦♦ 20
3
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2
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939
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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 14 months ago by rsafavi • 40
1
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1
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1.0k
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1
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pysam pileup: what reads appear in the pileup?
software genome alignment pysam sequencing written 14 months ago by aostern • 30
1
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1
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513
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1
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pysam: Use read ID to access location
python pysam bam file written 15 months ago by bd2810 • 0
7
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2
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1.7k
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5 follow
2
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How to count the total aligned bases in BAM?
python bam pysam pybedtools written 15 months ago by vw • 20
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690
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How to compute target aligned reads/total aligned reads (read enrichment) with Python?
bed bam pybedtools pysam written 16 months ago by vw • 20
4
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1
answer
701
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5 follow
1
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output differents value between samtools depth and pysam
python pysam written 16 months ago by electronsource75 • 10 • updated 16 months ago by Devon Ryan ♦ 91k
5
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1
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11k
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7 follow
1
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python script error: ImportError: No module named pysam
.py overlapsignature pysam pythonscript written 16 months ago by jaqx008 • 50 • updated 16 months ago by Carlos Borroto • 1.8k
3
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1
answer
1.1k
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1
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calculate fragments depth with pysam
genome python samtools pysam written 16 months ago by electronsource75 • 10
2
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2
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1.2k
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2
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Pysam fetch for records not exists in VCF files
pysam fetch written 2.9 years ago by always_learning • 980 • updated 16 months ago by Vasisht • 170
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