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pysam pileup doesn't work when contig name is specified?
pysam pileup coverage depth written 8 weeks ago by dp • 40
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226
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Pysam pileup dropping reads
pysam pileup written 6 months ago by yryan • 0
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201
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Call all insertions and deletions in bam file
pileup written 7 months ago by Mick • 10
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565
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Difference between Pysam Pileup and Fetch
reads bam pysam pileup written 10 months ago by aalith • 10 • updated 8 months ago by castaway1990 • 0
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415
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1
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Finding all bases at a specific genomic position
pysam pileup written 12 months ago by dodani • 0
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samtools mpileup keeps making an empty file
samtools pileup written 19 months ago by James Reeve • 100 • updated 19 months ago by gab • 20
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5 follow
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Pileup To Vcf Format
vcf pileup written 9.3 years ago by Pri • 20 • updated 21 months ago by Mbillah • 110
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5 follow
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Popoolation variance-sliding.pl output shows only zero value
popoolation tajima's pi samtools pileup tajima's d written 3.1 years ago by bruseq • 40 • updated 21 months ago by alex.zaccaron • 170
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Samtools 1.3 mpileup result < >
next-gen samtools rna-seq pileup sequencing written 4.5 years ago by yanweng • 40 • updated 22 months ago by RamRS ♦ 28k
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Mapping Reads Back To Assembly Contigs To Generate Pileup
pileup bwa coverage written 8.4 years ago by Sen • 0 • updated 22 months ago by Biostar ♦♦ 20
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Generating pileup from .bam file
genome indels pileup written 2.3 years ago by ajuric101 • 30
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SRA tootkit to download pileup formats using SRR accessions
sratoolkit next-gen pileup sequencing written 2.3 years ago by Paul • 80
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611
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pileup vs. IGV insertion locations
pileup igv written 2.3 years ago by blur • 120
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635
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How to calculate standard deviation of coverage for each scaffold in a pileup file?
perl coverage pileup sequencing written 2.4 years ago by PollardMD • 0
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Finding SNPs in population data: help with pipeline
genome population snp pileup written 3.3 years ago by Alex • 0 • updated 2.7 years ago by Pierre Lindenbaum ♦ 129k
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7 follow
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Samtools Mpileup And Overlapping Paired-End Reads
paired-end pileup rna-seq written 6.7 years ago by alpha2zee • 120 • updated 2.7 years ago by Owen S. • 350
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Pysam read reference positions and sequence do not match
samtools pysam pileup tview written 2.8 years ago by rlorigro • 0 • updated 2.8 years ago by Biostar ♦♦ 20
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Nucleotide coverage if >5 reads
alignment sequence pileup written 2.8 years ago by Vca80553 • 0 • updated 2.8 years ago by Pierre Lindenbaum ♦ 129k
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808
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Samtools pileup problem.
rna-seq pileup written 2.9 years ago by salvatore.digiorgio • 10
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1
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Samtools mpileup output: missing fields?
rnaseq samtools pileup mpileup written 2.9 years ago by cjaln • 0 • updated 2.9 years ago by John Marshall ♦ 2.0k
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pileup format: what's the difference between upper and lower case?
samtools pileup written 3.2 years ago by blur • 120 • updated 3.2 years ago by Devon Ryan ♦ 96k
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Filter pileup file for completeness
filter samtools completeness pileup written 3.9 years ago by AP • 100
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What does "pileup" mean in the context of MACS2 peak caller?
macs2 chip-seq pileup written 3.3 years ago by ariel.balter • 140 • updated 3.3 years ago by Santosh Anand ♦ 5.1k
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filtering pileup file with samtools for SomaticSniper
somaticsniper samtools snp pileup written 4.9 years ago by TriS • 4.2k • updated 3.7 years ago by guangxujin • 0
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Pileup format parsing difficulty
samtools pileup written 3.8 years ago by maheetha.b • 70 • updated 3.8 years ago by John Marshall ♦ 2.0k
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5 follow
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Genomic Coverage - Samtool's undocumented "depth" verses the poorly documented pileup.
pileup samtools coverage mpileup depth written 6.0 years ago by John ♦ 12k • updated 4.5 years ago by Shicheng Guo • 8.3k
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(samtools) Filtering and interpreting >100 QUAL scores
vcf phred-scaled qual samtools pileup written 4.5 years ago by umn_bist • 370 • updated 4.5 years ago by Brice Sarver • 3.5k
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understanding pysam pileup()
pysam pileup written 4.6 years ago by geek_y ♦ 11k
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Calculate nucleotide frequency for a position in a bam file using Bio::DB Perl module
perl bioperl pileup myposts written 4.8 years ago by Sameer Chavan • 0
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3
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How To Pile Up Multiple Bed Files Into 1 File
bed intersect sam bam pileup written 8.2 years ago by Hanfei Sun • 60 • updated 4.8 years ago by Biostar ♦♦ 20
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