| faOneRecord |
faOneRecord in.fa recordName |
Extract a single record from a fasta file |
| twoBitInfo |
twoBitInfo input.2bit output.tab |
Get information about sequences in a .2bit file |
| faCmp |
faCmp [options] a.fa b.fa |
Compare two fasta files |
| netSyntenic |
netSyntenic in.net out.net |
Add synteny info to net. |
| pslReps |
pslReps in.psl out.psl out.psr |
Analyse repeats and generate genome wide bestalignments from a sorted set of local alignments |
| bigWigToWig |
bigWigToWig in.bigWig out.wig |
Convert bigWig to wig. This will keep more of the same structure of theoriginal wig than bigWigToBedGraph does, but still will break up large stepped sectionsinto smaller ones. |
| genePredSingleCover |
genePredSingleCover [options] inGenePred outGenePred |
Create single-coverage genePred files |
| colTransform |
colTransform column input.tab addFactor mulFactor output.tab |
colTransform - Add and/or multiply column by constant. |
| netClass |
netClass [options] in.net tDb qDb out.net |
Add classification info to net |
| crTreeSearchBed |
crTreeSearchBed file.bed index.cr chrom start end |
Search a crTree indexed bed file and print all items that overlap query. |
| hgFindSpec |
hgFindSpec [options] orgDir database hgFindSpec hgFindSpec.sql hgRoot |
Create hgFindSpec table from trackDb.ra files. |
| maskOutFa |
maskOutFa in.fa maskFile out.fa.masked |
Produce a masked .fa file given an unmasked .fa anda RepeatMasker .out file, or a .bed file to mask on. |
| wigEncode |
wigEncode [options] wigInput wigFile wibFile |
Convert Wiggle ascii data to binary format |
| checkHgFindSpec |
checkHgFindSpec database [options | termToSearch] |
Test and describe search specs in hgFindSpec tables. |
| nibFrag |
nibFrag [options] file.nib start end strand out.fa |
Extract part of a nib file as .fa (all bases/gaps lower case by default) |
| splitFile |
splitFile source linesPerFile outBaseName |
Split up a file |
| chainPreNet |
chainPreNet in.chain target.sizes query.sizes out.chain |
Remove chains that don't have a chance of being netted |
| headRest |
headRest count fileName |
Return all *but* the first N lines of a file. |
| chopFaLines |
chopFaLines in.fa out.fa |
Read in FA file with long lines and rewrite it with shorter lines |
| chainSplit |
chainSplit outDir inChain(s) |
Split chains up by target or query sequence |