| wigCorrelate |
wigCorrelate one.wig two.wig ... n.wig |
Produce a table that correlates all pairs of wigs |
| gtfToGenePred |
gtfToGenePred gtf genePred |
Convert a GTF file to a genePred |
| liftOverMerge |
liftOverMerge oldFile newFile |
Merge multiple regions in BED 5 filesgenerated by liftOver -multiple |
| rowsToCols |
rowsToCols in.txt out.txt |
Convert rows to columns and vice versa in a text file. |
| axtChain |
axtChain -linearGap=loose in.axt tNibDir qNibDir out.chain |
Chain together axt alignments. |
| bedToGenePred |
bedToGenePred bedFile genePredFile |
Convert bed format files to genePred format |
| chainFilter |
chainFilter file(s) |
Filter chain files. Output goes to standard out. |
| faFilter |
faFilter [options] in.fa out.fa |
Filter fasta records, selecting ones that match the specified conditions |
| bigBedSummary |
bigBedSummary file.bb chrom start end dataPoints |
Extract summary information from a bigBed file. |
| bigWigAverageOverBed |
bigWigAverageOverBed in.bw in.bed out.tab |
Compute average score of big wig over each bed, which may have introns. |
| chainStitchId |
chainStitchId in.chain out.chain |
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) |
Extend length of entries in bed 6+ data to be at least the given length, taking strand directionality into account. |
| chainToPsl |
chainToPsl in.chain tSizes qSizes target.lst query.lst out.psl |
Convert chain file to psl format |
| twoBitMask |
twoBitMask input.2bit maskFile output.2bit |
Apply masking to a .2bit file, creating a new .2bit file |
| pslCDnaFilter |
pslCDnaFilter [options] inPsl outPsl |
Filter cDNA alignments in psl format |
| chainNet |
chainNet in.chain target.sizes query.sizes target.net query.net |
Make alignment nets out of chains |
| catUncomment |
catUncomment file(s) |
catUncomment - Concatenate input removing lines that start with '#'Output goes to stdout |
| ldHgGene |
ldHgGene database table file(s).gff |
Load database with gene predictions from a gff file. |
| catDir |
catDir dir(s) |
catDir - concatenate files in directory to stdout.For those times when too many files for cat to handle. |
| hgsqldump |
hgsqldump [OPTIONS] database [tables] |
Execute mysqldump using passwords from .hg.conf |