| bigBedToBed |
bigBedToBed input.bb output.bed |
Convert from bigBed to ascii bed format. |
| gff3ToGenePred |
gff3ToGenePred inGff3 outGp |
Convert a GFF3 file to a genePred file |
| bedGraphToBigWig |
bedGraphToBigWig in.bedGraph chrom.sizes out.bw |
Convert a bedGraph file to bigWig format. |
| bigWigToBedGraph |
bigWigToBedGraph in.bigWig out.bedGraph |
Convert from bigWig to bedGraph format. |
| twoBitToFa |
twoBitToFa input.2bit output.fa |
Convert all or part of .2bit file to fasta |
| genePredToBed |
genePredToBed in.genePred out.bed |
Convert from genePred to bed format |
| lavToAxt |
lavToAxt in.lav tNibDir qNibDir out.axt |
Convert blastz lav file to an axt file (which includes sequence) |
| wiggletools |
wiggletools sum [bigwig files...] |
Merge BigWig files |
| bedtools bedtobam |
bedtools bedtobam [OPTIONS] -i <bed/gff/vcf> -g <genome> |
Converts feature records to BAM format (also known as bedToBam) |
| bedtools bed12tobed6 |
bedtools bed12tobed6 [OPTIONS] -i <bed12> |
Splits BED12 features into discrete BED6 features (also know as bed12ToBed6) |