| wigCorrelate |
wigCorrelate one.wig two.wig ... n.wig |
Produce a table that correlates all pairs of wigs |
| mafsInRegion |
mafsInRegion regions.bed out.maf|outDir in.maf(s) |
mafsInRegion - Extract MAFS in a genomic region |
| bedRemoveOverlap |
bedRemoveOverlap in.bed out.bed |
bedRemoveOverlap - Remove overlapping records from a (sorted) bed file. Gets rid of`the smaller of overlapping records. |
| twoBitToFa |
twoBitToFa input.2bit output.fa |
Convert all or part of .2bit file to fasta |
| gtfToGenePred |
gtfToGenePred gtf genePred |
gtfToGenePred - convert a GTF file to a genePred |
| liftOverMerge |
liftOverMerge oldFile newFile |
liftOverMerge - Merge multiple regions in BED 5 filesgenerated by liftOver -multiple |
| mafSpeciesSubset |
mafSpeciesSubset in.maf species.lst out.maf |
mafSpeciesSubset - Extract a maf that just has a subset of species. |
| rowsToCols |
rowsToCols in.txt out.txt |
rowsToCols - Convert rows to columns and vice versa in a text file. |
| mafToPsl |
mafToPsl querySrc targetSrc in.maf out.psl |
mafToPsl - Convert maf to psl format |
| axtChain |
axtChain -linearGap=loose in.axt tNibDir qNibDir out.chain |
axtChain - Chain together axt alignments. |
| mafOrder |
mafOrder mafIn order.lst mafOut |
mafOrder - order components within a maf file |
| chainFilter |
chainFilter file(s) |
chainFilter - Filter chain files. Output goes to standard out. |
| bigBedSummary |
bigBedSummary file.bb chrom start end dataPoints |
bigBedSummary - Extract summary information from a bigBed file. |
| faFilter |
faFilter [options] in.fa out.fa |
faFilter - Filter fa records, selecting ones that match the specified conditions |
| chainStitchId |
chainStitchId in.chain out.chain |
chainStitchId - Join chain fragments with the same chain ID into a singlechain per ID. Chain fragments must be from same original chain butmust not overlap. Chain fragment scores are summed. |
| bedExtendRanges |
bedExtendRanges database length files(s) |
bedExtendRanges - extend length of entries in bed 6+ data to be at least the given length,taking strand directionality into account. |
| twoBitMask |
twoBitMask input.2bit maskFile output.2bit |
twoBitMask - apply masking to a .2bit file, creating a new .2bit file |
| bedToGenePred |
bedToGenePred bedFile genePredFile |
Too few arguments:bedToGenePred - convert bed format files to genePred format |
| bigWigAverageOverBed |
bigWigAverageOverBed in.bw in.bed out.tab |
bigWigAverageOverBed - Compute average score of big wig over each bed, which may have introns. |
| chainToPsl |
chainToPsl in.chain tSizes qSizes target.lst query.lst out.psl |
chainToPsl - Convert chain file to psl format |