| netChainSubset |
netChainSubset in.net in.chain out.chain |
Create chain file with subset of chains that appear in the net |
| faSplit |
faSplit how input.fa count outRoot |
Split an fa file into several files. |
| faCount |
faCount file(s).fa |
Count base statistics and CpGs in fasta files. |
| fastqToFa |
fastqToFa [options] in.fastq out.fa |
Convert from fastq to fasta format. |
| stringify |
stringify [options] in.txt |
Convert file to C strings |
| tickToDate |
tickToDate ticks |
Convert seconds since 1970 to time and date |
| chainMergeSort |
chainMergeSort file(s) |
Combine sorted files into larger sorted file |
| pslStats |
pslStats [options] psl statsOut |
Collect statistics from a psl file. |
| toUpper |
toUpper inFile outFile |
Convert lower case to upper case in file. Leave other chars alone |
| wordLine |
wordLine inFile(s) |
Chop up words by white space and output them with oneword to each line. |
| bedToBigBed |
bedToBigBed in.bed chrom.sizes out.bb |
Convert bed file to bigBed. |
| hgLoadOut |
hgLoadOut database file(s).out |
Load RepeatMasker .out files into database |
| netToAxt |
netToAxt in.net in.chain target.2bit query.2bit out.axt |
Convert net (and chain) to axt. |
| pslDropOverlap |
pslDropOverlap in.psl out.psl |
Deletes all overlapping self alignments. |
| validateManifest |
validateManifest |
Validates the ENCODE3 manifest.txt file. Calls validateFiles on each file in the manifest.Exits with a zero status for no errors detected and non-zero for errors. Writes Error messages to stderr |
| autoDtd |
autoDtd in.xml out.dtd out.stats |
Give this a XML document to look at and it will come up with a DTDto describe it. |
| clstr_merge.pl |
clstr_merge.pl db2new.clstr db3new.clstr > db23new.clstr |
It merges two or more .clstr files. The cluster orders need to be identical. |
| tdbQuery |
tdbQuery sqlStatement |
Query the trackDb system using SQL syntax. |
| validateFiles |
validateFiles -chromInfo=FILE -options -type=FILE_TYPE file1 [file2 [...]] |
Validates the format of different genomic files.Exits with a zero status for no errors detected and non-zero for errors.Uses filename 'stdin' to read from stdin.Automatically decompresses Files in .gz, .bz2, .zip, .Z format.Accepts multiple input files of the same type.Writes Error messages to stderr |
| newProg |
newProg progName description words |
Make a new C source skeleton. |