Difference in SNP number in the output of Poolfreqdiff and Popoolation2 using the same filters.
The program Poolfreqdiff is an alternative method to the CMH implemented in the program Popoolation2 and commonly used in pool-seq studies. I noticed that the program Poolfreqdiff gives output for fewer SNPs (25K) than Popoolation2 (47K) using the same filters. Does anyone know why?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Alternatives to snpflip to find ambigious and flipped snps
written by d.s.zimmerman •
-
Options for assigning cell labels to barcodes from CITE-seq experiment
written by Chris Dean •
-
Inconsistencies and QQ plot inflation in CMH Test Results for case-control Pool Seq: Underestimatin…
written by C •
-
STAR: Two-Pass mapping, Should SJ.out.tab files be filtered out or not?
written by conor93
-
NGSadmix
written by Harry •
-
How exactly does diffBind count reads?
written by iamjli •
-
Input file MULTIPOOL - reference allele counts from mpileup/bam
written by pedroamandrade •
-
Why estimate fragment size of ChIP-seq with SPP when using Macs2 for peak calling?
written by colin.kern
-
5'adaptor trimming of microRNA sequence data
written by evimeng •
-
Finding Mirna Seed Region By Aligning Mirna And Seeing That Positions 2-8 Hit Fewer Snps
written by Click downvote
