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3
votes
1
answer
124
views
1
answer
unmapped reads with pysam
pysam written 17 days ago by grant.hovhannisyan • 1.4k
0
votes
0
answers
132
views
0
answers
Analogy of exifread library in pysam for bam and vcf header files
vcf bam bcftools pysam htslib written 28 days ago by aiteteji • 10
3
votes
1
answer
87
views
1
answer
Pysam VariantFile.fetch() without specifying contig
vcf python pysam written 5 weeks ago by ricardoguerreiro2121 • 20
3
votes
1
answer
307
views
1
answer
pysam difference between template_length and reference_length
genome next-gen pysam written 3 months ago by Medhat ♦ 8.1k • updated 3 months ago by Devon Ryan ♦ 88k
0
votes
0
answers
193
views
0
answers
pysam: How do I type an AlignedSegment in Cython?
cython pysam written 3 months ago by Click downvote • 650 • updated 3 months ago by Biostar ♦♦ 20
0
votes
0
answers
203
views
0
answers
How to ignore truncation error with PySam?
python sam alignment mapping pysam written 4 months ago by O.rka • 70 • updated 3 months ago by Biostar ♦♦ 20
0
votes
0
answers
215
views
0
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appropriate way to use pysam.depth
python pysam written 4 months ago by Medhat ♦ 8.1k
2
votes
2
answers
1.9k
views
2
answers
Problem iterating through BAM file using pysam
python sam bam forloop pysam written 3.0 years ago by c9r1y • 0 • updated 5 months ago by RamRS ♦ 20k
7
votes
3
answers
5.5k
views
3
answers
cannot import pysam. Module has no attribute error
samtools api python pysam written 3.6 years ago by QVINTVS_FABIVS_MAXIMVS • 2.2k • updated 5 months ago by RamRS ♦ 20k
1
vote
0
answers
1.3k
views
0
answers
pysam truncated file error
python samtools pysam written 19 months ago by pupatel • 0 • updated 5 months ago by Biostar ♦♦ 20
3
votes
2
answers
418
views
2
answers
Get all the nucleotides from a bam file that is aligning to specific position in the genome
genome samtools alignment position pysam written 6 months ago by rsafavi • 40
1
vote
1
answer
538
views
1
answer
pysam pileup: what reads appear in the pileup?
software genome alignment pysam sequencing written 7 months ago by aostern • 30
1
vote
1
answer
252
views
1
answer
pysam: Use read ID to access location
python pysam bam file written 8 months ago by bd2810 • 0
5
votes
2
answers
987
views
2
answers
How to count the total aligned bases in BAM?
python bam pysam pybedtools written 8 months ago by vw • 10
0
votes
0
answers
416
views
0
answers
How to compute target aligned reads/total aligned reads (read enrichment) with Python?
bed bam pybedtools pysam written 8 months ago by vw • 10
4
votes
1
answer
456
views
5 follow
1
answer
output differents value between samtools depth and pysam
python pysam written 9 months ago by electronsource75 • 10 • updated 9 months ago by Devon Ryan ♦ 88k
5
votes
1
answer
4.8k
views
7 follow
1
answer
python script error: ImportError: No module named pysam
.py overlapsignature pysam pythonscript written 9 months ago by jaqx008 • 40 • updated 9 months ago by Carlos Borroto • 1.8k
3
votes
1
answer
663
views
1
answer
calculate fragments depth with pysam
genome python samtools pysam written 9 months ago by electronsource75 • 10
2
votes
2
answers
986
views
2
answers
Pysam fetch for records not exists in VCF files
pysam fetch written 2.3 years ago by always_learning • 950 • updated 9 months ago by Vasisht • 150
1
vote
1
answer
961
views
1
answer
iterate over reads in .SAM file with pysam - IndexError: list index out of range
python pysam sam written 10 months ago by Florian BERNARD • 20 • updated 10 months ago by Pierre Lindenbaum ♦ 116k
5
votes
2
answers
1.1k
views
5 follow
2
answers
How to use pysam to execute "samtools fastq xxx.sam>xxx.fastq"
samtools pysam written 11 months ago by Zhixue • 10
0
votes
0
answers
317
views
0
answers
Estimate Fragment Size from Single End ChipSeq with (pysam, htseq lib or deeptools API)
htseq deeptools pysam written 12 months ago by ZheFrench • 190
15
votes
3
answers
2.4k
views
3
answers
Pysam is giving - ValueError: reference_id -1 out of range 0<=tid<65334. Any suggestions?
sam bam pysam reference_id written 2.7 years ago by kirannbishwa01 • 930 • updated 13 months ago by Matt Shirley ♦ 8.8k
0
votes
0
answers
1.1k
views
0
answers
Pysam read reference positions and sequence do not match
samtools pysam pileup tview written 16 months ago by rlorigro • 0 • updated 15 months ago by Biostar ♦♦ 20
0
votes
0
answers
774
views
0
answers
Create small BAM file with pysam and iterate over reads
samtool bam pysam written 15 months ago by lebedana21 • 0
0
votes
1
answer
540
views
1
answer
Error in pysam: trying to read BAM file using CYTHON
next-gen alignment pysam written 16 months ago by ammarsabir15 • 50 • updated 16 months ago by Devon Ryan ♦ 88k
0
votes
1
answer
689
views
1
answer
pysam not plotting exact values for coverage
alignment pysam coverage written 17 months ago by ammarsabir15 • 50 • updated 17 months ago by Devon Ryan ♦ 88k
1
vote
0
answers
849
views
0
answers
Error during htseq-count
htseq-count star pysam written 17 months ago by baffiak1902 • 10
6
votes
1
answer
2.6k
views
1
answer
pysam: filtering reads based on flag
python samtools pysam hts written 3.6 years ago by QVINTVS_FABIVS_MAXIMVS • 2.2k • updated 19 months ago by Biostar ♦♦ 20
2
votes
1
answer
532
views
1
answer
Extract R2F1 reads
samtools pysam structural variation written 19 months ago by IP • 530
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