| faFilterN |
faFilterN in.fa out.fa maxPercentN |
Get rid of sequences with too many N's |
| checkAgpAndFa |
checkAgpAndFa in.agp in.fa |
Take a .agp file and .fa file and ensure that they are in synch |
| localtime |
localtime |
Convert unix timestamp to date string |
| faTrans |
faTrans in.fa out.fa |
Translate DNA .fa file to peptide |
| bedItemOverlapCount |
sort bedFile.bed | bedItemOverlapCount [options] <database> stdin |
Count number of times a base is overlapped by theitems in a bed file. Output is bedGraph 4 to stdout. |
| faSize |
faSize file(s).fa |
Print total base count in fa files. |
| mrnaToGene |
mrnaToGene [options] psl genePredFile |
Convert PSL alignments of mRNAs to gene annotations |
| chainToAxt |
chainToAxt in.chain tNibDirOr2bit qNibDirOr2bit out.axt |
Convert from chain to axt file |
| pslPartition |
pslPartition [options] pslFile outDircreated under outDir to prevent slow access to huge directories. |
Split PSL files into non-overlapping sets |
| sqlToXml |
sqlToXml database dumpSpec.od output.xml |
Dump out all or part of a relational database to XML, guidedby a dump specification. See sqlToXml.doc for additional information. |
| faToTwoBit |
faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit |
Convert DNA from fasta to 2bit format |
| clstr_rev.pl |
clstr_rev.pl nr90.clstr nr60.clstr > nr60_from90.clstr |
It combines a .clstr file with its parent .clstr file |
| faFrag |
faFrag in.fa start end out.fa |
Extract a piece of DNA from a fasta file. |
| pslLiftSubrangeBlat |
pslLiftSubrangeBlat isPsl outPsl |
Lift PSLs from blat subrange alignments |
| qacToWig |
qacToWig in.qac outFileOrDir |
Convert from compressed quality score format to wiggle format. |
| bedIntersect |
bedIntersect a.bed b.bed output.bed |
Intersect two bed files |
| dbSnoop |
dbSnoop database output |
Produce an overview of a database. |
| qaToQac |
qaToQac in.qa out.qac |
Convert from uncompressed to compressedquality score format. |
| bedClip |
bedClip input.bed chrom.sizes output.bed |
Remove lines from bed file that refer to off-chromosome places. |
| qacAgpLift |
qacAgpLift scaffoldToChrom.agp scaffolds.qac chrom.qac |
Use AGP to combine per-scaffold qac into per-chrom qac. |