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6
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3
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212
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3
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Generating pileup from .bam file
genome indels pileup written 7 weeks ago by ajuric101 • 10
1
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0
answers
96
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0
answers
SRA tootkit to download pileup formats using SRR accessions
sratoolkit next-gen pileup sequencing written 10 weeks ago by Paul • 50
0
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0
answers
98
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0
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pileup vs. IGV insertion locations
pileup igv written 10 weeks ago by blur • 90
0
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0
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244
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0
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How to calculate standard deviation of coverage for each scaffold in a pileup file?
perl coverage pileup sequencing written 3 months ago by PollardMD • 0
2
votes
2
answers
508
views
2
answers
Popoolation variance-sliding.pl output shows only zero value
popoolation tajima's pi samtools pileup tajima's d written 11 months ago by divya • 10 • updated 4 months ago by antaky • 0
0
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1
answer
617
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1
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Finding SNPs in population data: help with pipeline
genome population snp pileup written 13 months ago by Alex • 0 • updated 6 months ago by Pierre Lindenbaum ♦ 108k
7
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2
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4.4k
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7 follow
2
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Samtools Mpileup And Overlapping Paired-End Reads
paired-end pileup rna-seq written 4.6 years ago by alpha2zee • 100 • updated 7 months ago by Owen S. • 330
0
votes
0
answers
534
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0
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Pysam read reference positions and sequence do not match
samtools pysam pileup tview written 8 months ago by rlorigro • 0 • updated 7 months ago by Biostar ♦♦ 20
5
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1
answer
496
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5 follow
1
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Nucleotide coverage if >5 reads
alignment sequence pileup written 8 months ago by Vca80553 • 0 • updated 8 months ago by Pierre Lindenbaum ♦ 108k
0
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1
answer
265
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1
answer
Samtools pileup problem.
rna-seq pileup written 9 months ago by salvatore.digiorgio • 10
4
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1
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483
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1
answer
Samtools mpileup output: missing fields?
rnaseq samtools pileup mpileup written 9 months ago by cjaln • 0 • updated 9 months ago by John Marshall • 1.2k
1
vote
1
answer
421
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1
answer
pileup format: what's the difference between upper and lower case?
samtools pileup written 13 months ago by blur • 90 • updated 13 months ago by Devon Ryan ♦ 81k
0
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1
answer
457
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1
answer
Filter pileup file for completeness
filter samtools completeness pileup written 21 months ago by AP • 80
2
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1
answer
1.1k
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1
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What does "pileup" mean in the context of MACS2 peak caller?
macs2 chip-seq pileup written 14 months ago by ariel.balter • 130 • updated 14 months ago by Santosh Anand • 3.5k
1
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2
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1.7k
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2
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filtering pileup file with samtools for SomaticSniper
somaticsniper samtools snp pileup written 2.7 years ago by TriS • 3.4k • updated 19 months ago by guangxujin • 0
1
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1
answer
591
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1
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Pileup format parsing difficulty
samtools pileup written 20 months ago by maheetha.b • 50 • updated 20 months ago by John Marshall • 1.2k
1
vote
2
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806
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2
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Samtools 1.3 mpileup result < >
next-gen samtools rna-seq pileup sequencing written 2.3 years ago by yanweng • 20 • updated 2.3 years ago by alebuenosm • 20
15
votes
3
answers
5.5k
views
5 follow
3
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Genomic Coverage - Samtool's undocumented "depth" verses the poorly documented pileup.
pileup samtools coverage mpileup depth written 3.9 years ago by John ♦ 12k • updated 2.4 years ago by Shicheng Guo • 4.9k
7
votes
1
answer
2.2k
views
1
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(samtools) Filtering and interpreting >100 QUAL scores
vcf phred-scaled qual samtools pileup written 2.4 years ago by umn_bist • 310 • updated 2.4 years ago by Brice Sarver • 2.4k
1
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1
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2.8k
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1
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understanding pysam pileup()
pysam pileup written 2.5 years ago by geek_y ♦ 8.6k
0
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0
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1.7k
views
0
answers
Calculate nucleotide frequency for a position in a bam file using Bio::DB Perl module
perl bioperl pileup myposts written 2.7 years ago by Sameer Chavan • 0
1
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3
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2.3k
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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 6.1 years ago by Hanfei Sun • 60 • updated 2.7 years ago by Biostar ♦♦ 20
1
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1
answer
3.6k
views
1
answer
Masked Or Unmasked Dna Reference For Sam2Vcf.Pl
vcf samtools pileup written 7.1 years ago by Pi • 510 • updated 2.8 years ago by Biostar ♦♦ 20
2
votes
1
answer
1.3k
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1
answer
Samtools mpileup not providing correct count info
simulation samtools mpileup pileup written 2.9 years ago by jgbradley1 • 80
5
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1
answer
1.3k
views
1
answer
Rsamtools::pileup gives inconsistent number of reads
rsamtools pileup written 3.3 years ago by inesdesantiago • 140
3
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1
answer
2.9k
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1
answer
Is the MACS pileup output normalized
macs normalization pileup written 3.7 years ago by ivoryec • 60
3
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1
answer
2.4k
views
1
answer
meaning of new symbols in samtools mpileup format?
samtools snp pileup htslib written 3.8 years ago by Dejian • 1.2k • updated 3.8 years ago by Devon Ryan ♦ 81k
0
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0
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1.2k
views
0
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Bio-SamTools pileup method
bioperl bio-samtools pileup written 3.9 years ago by Max Ivon • 110
0
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0
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1.4k
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0
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Calculating Mutation Rate Using Mpileup Files
mutation samtools mpileup pileup written 4.3 years ago by QVINTVS_FABIVS_MAXIMVS • 2.1k
2
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1
answer
1.3k
views
1
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Samtools Pileup Of Millions Of Reads From A Single Amplicon
samtools pileup sequencing written 4.3 years ago by Sebastian • 10 • updated 4.3 years ago by Christian • 2.6k
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