| mafSplit |
mafSplit splits.bed outRoot file(s).maf |
Split multiple alignment files |
| mafsInRegion |
mafsInRegion regions.bed out.maf|outDir in.maf(s) |
Extract MAFs in genomic regions |
| mafSpeciesSubset |
mafSpeciesSubset in.maf species.lst out.maf |
Extract a maf that just has a subset of species. |
| mafToPsl |
mafToPsl querySrc targetSrc in.maf out.psl |
Convert maf to psl format |
| mafOrder |
mafOrder mafIn order.lst mafOut |
Order components within a maf file |
| mafRanges |
mafRanges in.maf db out.bed |
Extract ranges of target (or query) coverage from maf and output as BED 3 (e.g. for processing by featureBits). |
| genePredToMafFrames |
genePredToMafFrames [options] targetDb maf mafFrames geneDb1 genePred1 [geneDb2 genePred2...] |
Create frame annotations for one or more components of a MAF. It is significantly faster to process multiple gene sets in the same"run, as 95% of the CPU time is spent reading the MAF |
| mafCoverage |
mafCoverage database mafFile |
Analyse coverage by maf files - chromosome bychromosome and genome-wide. |
| mafFrags |
mafFrags database track in.bed out.maf |
Collect MAFs from regions specified in a 6 column bed file |
| mafToAxt |
mafToAxt in.maf tName qName output |
Convert from maf to axt format |
| mafGene |
mafGene dbName mafTable genePredTable species.lst output |
Output protein alignments using maf and genePred |
| mafAddQRows |
mafAddQRows species.lst in.maf out.maf |
Add quality data to a maf |
| mafAddIRows |
mafAddIRows mafIn twoBitFile mafOut |
Add 'i' rows to a maf |
| axtToMaf |
axtToMaf in.axt tSizes qSizes out.maf |
Convert from axt to maf format |
| mafSplitPos |
mafSplitPos database size(Mbp) out.bed |
Pick positions to split multiple alignment input files |
| mafSpeciesList |
mafSpeciesList in.maf out.lst |
Scan maf and output all species used in it. |
| mafFetch |
mafFetch db table overBed mafOut |
Get overlapping records from an MAF using an index table |
| mafFilter |
mafFilter file(s).maf |
Filter out maf files. Output goes to standard out |
| mafMeFirst |
mafMeFirst in.maf me.list out.maf |
Move component to top if it is one of the named ones.Useful in conjunction with mafFrags when you don't want the one withthe gene name to be in the middle. |
| mafFrag |
mafFrag database mafTrack chrom start end strand out.maf |
Extract maf sequences for a region from database |