Format Conversion

Function: Convert a bedGraph file to bigWig format.

Usage: bedGraphToBigWig [options] in.bedGraph chrom.sizes out.bw

Supported input format: bedGraph

Function: Convert from bigWig to bedGraph format.

Usage: bigWigToBedGraph in.bigWig out.bedGraph

Function: Convert a GTF file to a genePred

Usage: gtfToGenePred [options] gtf genePred

Function: Convert from bigBed to ascii bed format.

Usage: bigBedToBed [options] input.bb output.bed

Supported input format: bigBed

Function: Convert a GFF3 file to a genePred file

Usage: gff3ToGenePred inGff3 outGp

Function: Convert from genePred to bed format

Usage: genePredToBed in.genePred out.bed

Function: Convert all or part of .2bit file to fasta

Usage: twoBitToFa input.2bit output.fa

Function: Convert a bed file to bigBed format.

Usage: bedToBigBed in.bed chrom.sizes out.bb

Function: Convert from fastq to fasta format

Usage: fastqToFa [options] in.fastq out.fa

Supported input format: FASTQ

Function: Convert blastz lav file to an axt file (which includes sequence)

Usage: lavToAxt in.lav tNibDir qNibDir out.axt

Function: Converts feature records to BAM format (also known as bedToBam)

Usage: bedtools bedtobam [OPTIONS] -i <bed/gff/vcf> -g <genome>

Function: Splits BED12 features into discrete BED6 features (also know as bed12ToBed6)

Usage: bedtools bed12tobed6 [OPTIONS] -i <bed12>