bed2x

Functions

• get upstream/downstream/intron/exon/promoter/tts/tss/utr3/utr5/cds annotation bed based on input bed12/bed6 bigbed/tabix/gzip/ascii files.
• fetch cDNA sequence for bed12 format file.
• support stdin/stdout pipe

Install

Install from go

GO111MODULE=on go get github.com/nimezhu/bed2x/...

Download Binaries

Download pre-compiled files for Linux, Windows or Mac OS X from release.

Usage Examples

bed2x exon [file.bb or file.bed or file.bed.gz]  > file.exon.bed
bed2x promoter file.bb | bed2x seq -g genome.2bit > file.promoter.fa
bed2x read file.bb | head -10 | bed2 seq -g http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit
bed2x read file.bb | head -10 | bed2 seq -g hg19