| blastXmlToPsl |
blastXmlToPsl [options] blastXml psl |
Convert blast XML output to PSLs |
| pslFilter |
pslFilter in.psl out.psl |
Filter out psl file |
| pslSwap |
pslSwap [options] inPsl outPsl |
Swap target and query in psls |
| inner_distance.py |
inner_distance.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o output -r hg19.refseq.bed12 |
Calculate inner distance between read pairs. |
| crTreeIndexBed |
crTreeIndexBed in.bed out.cr |
Create an index for a bed file. |
| featureBits |
featureBits database table(s) |
Correlate tables via bitmap projections. |
| axtToPsl |
axtToPsl in.axt tSizes qSizes out.psl |
Convert axt to psl format |
| bigBedNamedItems |
bigBedNamedItems file.bb name output.bed |
Extract item of given name from bigBed |
| chainSwap |
chainSwap in.chain out.chain |
Swap target and query in chain |
| makeTableList |
makeTableList [assemblies] |
makeTableList - create/recreate tableList tables (cache of SHOW TABLES) |
| twoBitDup |
twoBitDup file.2bit |
Check to see if a twobit file has any identical sequences in it |
| pslPairs |
creates: <outFilePrefix>.pairs file |
Join paired ends in psl alignments |
| axtSwap |
axtSwap source.axt target.sizes query.sizes dest.axt |
Swap source and query in an axt file |
| pslRecalcMatch |
pslRecalcMatch in.psl targetSeq querySeq out.psl |
Recalculate match,mismatch,repMatch columns in psl file.This can be useful if the psl went through pslMap, or if you've addedlower-case repeat masking after the fact |
| chromGraphToBin |
chromGraphToBin in.tab out.chromGraph |
Make binary version of chromGraph. |
| xmlToSql |
xmlToSql in.xml in.dtd in.stats outDir |
Convert XML dump into a fairly normalized relational databasein the form of a directory full of tab-separated files and tablecreation SQL. You'll need to run autoDtd on the XML file first toget the dtd and stats files. |
| pslCheck |
pslCheck fileTbl(s) |
Validate PSL files |
| spacedToTab |
spacedToTab in.txt out.tab |
Convert fixed width space separated fields to tab separatedNote this requires two passes, so it can't be done on a pipe |
| bedWeedOverlapping |
bedWeedOverlapping weeds.bed input.bed output.bed |
Filter out beds that overlap a 'weed.bed' file. |
| checkCoverageGaps |
checkCoverageGaps database track1 ... trackN |
Check for biggest gap in coverage for a list of tracks.For most tracks coverage of 10,000,000 or more will indicate that there wasa mistake in generating the track. |