ZheLi

something wrong in bedtools getfasta -name

4

BEDtools version 2.26.0. Example as follow: mm10-NlaIII.bed: chr1 0 3000185 HIC_chr1_1@chr1:0-3000185 chr1 3000185 3000316 HIC_chr1_2@chr1:3000185-3000316 chr1 3000316 3000850 HIC_chr1_3@chr1:3000316-3000850 chr1 3000850 3001659 HIC_chr1_4@chr1:3000850-3001659 Code one with parameter -name: bedtools getfasta...

intersect result is wrong compare to bedtools intersect

11

I compare R function intersect in GenomicRanges package(terms RI), linux bedtools intersect(LI) and your tools, find that RI is the same as LI, but some wrong in your tools. I...