| blastToPsl |
blastToPsl [options] blastOutput psl |
Convert blast alignments to PSLs. |
| trfBig |
trfBig inFile outFile |
Mask tandem repeats on a big sequence file. |
| samtools faidx |
samtools faidx <ref.fasta> [region1 [...]] |
Index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. If no region is specified, faidx will index the file and create <ref.fasta>.fai on the disk. If regions are specified, the subsequences will be retrieved and printed to stdout in the FASTA format. |
| pslHisto |
pslHisto [options] what inPsl outHisto |
Collect counts on PSL alignments for making histograms. |
| faPolyASizes |
faPolyASizes in.fa out.tab |
Get poly A sizes |
| pslMrnaCover |
pslMrnaCover mrna.psl mrna.fa |
Make histogram of coverage percentage of mRNA in psl. |
| subChar |
subChar oldChar newChar file(s) |
Substitute one character for another throughout a file. |
| wigToBigWig |
wigToBigWig in.wig chrom.sizes out.bw |
Convert ascii format wig file (in fixedStep, variableStepor bedGraph format) to binary bigwig format. |
| oligoMatch |
oligoMatch oligos sequence output.bed |
Find perfect matches in sequence. |
| pslToPslx |
pslToPslx [options] in.psl qSeqSpec tSeqSpec out.pslx |
Convert from psl to pslx format, which includes sequences |
| clstr_merge_noorder.pl |
clstr_merge_noorder.pl db2new.clstr db3new.clstr > db23new.clstr |
It merges two or more .clstr files. The cluster orders do not have to be identical. |
| xmlCat |
xmlCat XXX |
Concatenate xml files together, stuffing all records inside a single outer tag. |
| netFilter |
netFilter in.net(s) |
Filter out parts of net. What passesfilter goes to standard output. Note a net is arecursive data structure. If a parent fails to passthe filter, the children are not even considered. |
| ameme |
ameme good=goodIn.fa [bad=badIn.fa] [numMotifs=2] [background=m1] [maxOcc=2] [motifOutput=fileName] [html=output.html] [gif=output.gif] [rcToo=on] [controlRun=on] [startScanLimit=20] [outputLogo] [constrainer=1] |
Find common patterns in DNA |
| chainAntiRepeat |
chainAntiRepeat tNibDir qNibDir inChain outChain |
Get rid of chains that are primarily the results of repeats and degenerate DNA |
| clstr_sort_by.pl |
Clstr_sort_by.pl input.clstr no > input_sort.clstr |
This script sort clusters in .clstr file by length, size |
| bedCoverage |
bedCoverage database bedFile |
Analyse coverage by bed files - chromosome bychromosome and genome-wide |
| genePredToFakePsl |
genePredToFakePsl db fileTbl pslOut cdsOut |
Create a psl of fake-mRNA aligned to gene-preds from a file or table. |
| hgLoadWiggle |
hgLoadWiggle [options] database track files(s).wig |
Load a wiggle track definition into database |
| ave |
ave file |
Compute average and basic stats |