| hgTrackDb |
hgTrackDb [options] org database trackDb trackDb.sql hgRoot |
Create trackDb table from text files.Note that the browser supports multiple trackDb tables, usuallyin the form: trackDb_YourUserName. Which particular trackDbtable the browser uses is specified in the hg.conf file foundeither in your home directory file '.hg.conf' or in the web server'scgi-bin/hg.conf configuration file with the setting: db.trackDb=trackDbsee also: src/product/ex.hg.conf discussion of this setting. |
| lavToPsl |
lavToPsl in.lav out.psl |
Convert blastz lav to psl format |
| raSqlQuery |
raSqlQuery raFile(s) query-options |
Do a SQL-like query on a RA file |
| netToBed |
netToBed in.net out.bed |
Convert target coverage of net to a bed file. |
| bedRestrictToPositions |
bedRestrictToPositions in.bed restrict.bed out.bed |
Filter bed file, restricting to only ones that match chrom/start/ends specified in restrict.bed file. |
| qacToQa |
qacToQa in.qac out.qa |
Convert from compressed to uncompressedquality score format. |
| hgLoadBed |
hgLoadBed database track files(s).bed |
Load a generic bed file into database |
| addCols |
addCols <fileName> |
Sum columns in a text file. |
| bedPileUps |
bedPileUps in.bed |
Find (exact) overlaps if any in bed input |
| faRc |
faRc in.fa out.fa |
Reverse complement a FA file |
| splitFileByColumn |
splitFileByColumn source outDir |
Split text input into files named by column value |
| faToTab |
faToTab infileName outFileName |
Convert fa file to tab separated file |
| hubCheck |
hubCheck http://yourHost/yourDir/hub.txt |
hubCheck - Check a track data hub for integrity. |
| paraSync |
paraSync {options} N R URL outPath |
paraSync 1.0paraSync - uses paraFetch to recursively mirror url to given path |
| estOrient |
estOrient [options] db estTable outPsl |
Convert ESTs so that orientation matches directory of transcription |
| linesToRa |
linesToRa in.txt out.ra |
Generate .ra format from lines with pipe-separated fields |
| pslSelect |
pslSelect [options] inPsl outPsl |
Select records from a PSL file. |
| subColumn |
subColumn column in.tab sub.tab out.tab |
Substitute one column in a tab-separated file. |
| cd-hit-div |
cd-hit-div -i input -o output -div n |
Divide a FASTA file into pieces |
| liftUp |
liftUp [-type=.xxx] destFile liftSpec how sourceFile(s) |
Change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf.bscore .tab .gdup .axt .chain .net, genePred, .wab, .bed, or .bed8 files toparent coordinate system. |