| axtSort |
axtSort in.axt out.axt |
Sort axt files |
| calc |
calc this + that * theOther / (a + b) |
Little command line calculator |
| pslMap |
pslMap [options] inPsl mapFile outPsl |
Map PSLs alignments to new targets using alignments ofthe old target to the new target. Given inPsl and mapPsl, wherethe target of inPsl is the query of mapPsl, create a new PSLwith the query of inPsl aligned to all the targets of mapPsl.If inPsl is a protein to nucleotide alignment and mapPsl is anucleotide to nucleotide alignment, the resulting alignment isnucleotide to nucleotide alignment of a hypothetical mRNA thatwould code for the protein. This is useful as it gives basealignments of spliced codons. A chain file may be used insteadmapPsl. |
| pslToChain |
pslToChain pslIn chainOut |
Convert psl records to chain records |
| countChars |
countChars char file(s) |
Count the number of occurences of a particular char |
| faToFastq |
faToFastq in.fa out.fastq |
Convert fa to fastq format, just faking quality values. |
| htmlCheck |
htmlCheck how url |
htmlCheck - Do a little reading and verification of html file |
| overlapSelect |
overlapSelect [options] selectFile inFile outFile |
Select records based on overlapping chromosome ranges |
| pslCat |
pslCat file(s) |
Concatenate psl files |
| pslPretty |
pslPretty in.psl target.lst query.lst pretty.out |
Convert PSL to human readable output |
| checkTableCoords |
checkTableCoords database [tableName] |
Check invariants on genomic coords in table(s). |
| chainSort |
chainSort inFile outFile |
Sort chains. By default sorts by score.Note this loads all chains into memory, so it is notsuitable for large sets. Instead, run chainSort onmultiple small files, followed by chainMergeSort. |
| gapToLift |
gapToLift [options] db liftFile.lft |
Create lift file from gap table(s) |
| nibSize |
nibSize nib1 [...] |
Print size of nibs |
| tailLines |
tailLines file tail |
Add tail to each line of file |
| pslSort |
pslSort dirs[1|2] outFile tempDir inDir(s) |
Merge and sort psCluster .psl output files |
| bedToPsl |
bedToPsl chromSizes bedFile pslFile |
Convert bed format files to psl format |
| chromGraphFromBin |
chromGraphFromBin in.chromGraph out.tab |
Convert chromGraph binary to ascii format. |
| faNoise |
faNoise inName outName transitionPpt transversionPpt insertPpt deletePpt chimeraPpt |
Add noise to fasta file |
| bedSort |
bedSort in.bed out.bed |
Sort a bed file by chromosome name and start position |