|
ucsc-coltransform
|
public |
Add and/or multiply column by constant.
|
2024-08-27 |
|
ucsc-hubpubliccheck
|
public |
checks that the labels in hubPublic match what is in the hub labels
|
2024-08-27 |
|
ucsc-validatefiles
|
public |
Validates the format of different genomic files.
|
2024-08-27 |
|
ucsc-axtchain
|
public |
Chain together axt alignments.
|
2024-08-27 |
|
ucsc-mafspeciessubset
|
public |
Extract a maf that just has a subset of species.
|
2024-08-27 |
|
ucsc-hgsqldump
|
public |
Execute mysqldump using passwords from .hg.conf
|
2024-08-27 |
|
ucsc-psltochain
|
public |
Convert psl records to chain records
|
2024-08-27 |
|
ucsc-autodtd
|
public |
Give this a XML document to look at and it will come up with a DTD
|
2024-08-27 |
|
ucsc-checkcoveragegaps
|
public |
Check for biggest gap in coverage for a list of tracks.
|
2024-08-27 |
|
ucsc-blasttopsl
|
public |
Convert blast alignments to PSLs.
|
2024-08-27 |
|
ucsc-bedcoverage
|
public |
Analyse coverage by bed files - chromosome by
|
2024-08-27 |
|
ucsc-pslcat
|
public |
concatenate psl files
|
2024-08-27 |
|
ucsc-bigbedinfo
|
public |
Show information about a bigBed file.
|
2024-08-27 |
|
ucsc-fastqtofa
|
public |
Convert from fastq to fasta format.
|
2024-08-27 |
|
ucsc-maftobigmaf
|
public |
Put ucsc standard maf file into bigMaf format
|
2024-08-27 |
|
ucsc-nibfrag
|
public |
Extract part of a nib file as .fa (all bases/gaps lower case by default)
|
2024-08-27 |
|
ucsc-estorient
|
public |
Read ESTs from a database and determine orientation based on estOrientInfo table or direction in gbCdnaInfo table. Update PSLs so that the strand reflects the direction of transcription. By default, PSLs where the direction can't be determined are dropped.
|
2024-08-27 |
|
ucsc-texthistogram
|
public |
Make a histogram in ascii
|
2024-08-27 |
|
ucsc-crtreeindexbed
|
public |
Create an index for a bed file.
|
2024-08-27 |
|
ucsc-genepredhisto
|
public |
get data for generating histograms from a genePred file.
|
2024-08-27 |
|
ucsc-chromgraphtobin
|
public |
Make binary version of chromGraph.
|
2024-08-27 |
|
ucsc-nettoaxt
|
public |
Convert net (and chain) to axt.
|
2024-08-27 |
|
ucsc-bedtopsl
|
public |
convert bed format files to psl format
|
2024-08-27 |
|
ucsc-chopfalines
|
public |
Read in FA file with long lines and rewrite it with shorter lines
|
2024-08-27 |
|
ucsc-oligomatch
|
public |
find perfect matches in sequence.
|
2024-08-27 |
|
ucsc-axtsort
|
public |
Sort axt files
|
2024-08-27 |
|
ucsc-paranodestop
|
public |
Shut down parasol node daemons on a list of machines
|
2024-08-27 |
|
ucsc-fanoise
|
public |
Add noise to .fa file
|
2024-08-27 |
|
ucsc-spacedtotab
|
public |
Convert fixed width space separated fields to tab separated
|
2024-08-27 |
|
ucsc-chainsplit
|
public |
Split chains up by target or query sequence
|
2024-08-27 |
|
ucsc-gaptolift
|
public |
create lift file from gap table(s)
|
2024-08-27 |
|
ucsc-pslpartition
|
public |
split PSL files into non-overlapping sets
|
2024-08-27 |
|
ucsc-fafiltern
|
public |
Get rid of sequences with too many N's
|
2024-08-27 |
|
ucsc-rasqlquery
|
public |
Do a SQL-like query on a RA file.
|
2024-08-27 |
|
ucsc-wigcorrelate
|
public |
Produce a table that correlates all pairs of wigs.
|
2024-08-27 |
|
ucsc-mafaddqrows
|
public |
Add quality data to a maf
|
2024-08-27 |
|
ucsc-bigbednameditems
|
public |
Extract item of given name from bigBed
|
2024-08-27 |
|
ucsc-gensub2
|
public |
version 12.18
|
2024-08-27 |
|
ucsc-genepredtomafframes
|
public |
create mafFrames tables from a genePreds
|
2024-08-27 |
|
ucsc-chaintopsl
|
public |
Convert chain file to psl format
|
2024-08-27 |
|
ucsc-hgspeciesrna
|
public |
Create fasta file with RNA from one species
|
2024-08-27 |
|
ucsc-wordline
|
public |
chop up words by white space and output them with one
|
2024-08-27 |
|
ucsc-parafetch
|
public |
try to fetch url with multiple connections
|
2024-08-27 |
|
ucsc-fetchchromsizes
|
public |
used to fetch chrom.sizes information from UCSC for the given <db>
|
2024-08-27 |
|
ucsc-validatemanifest
|
public |
Validates the ENCODE3 manifest.txt file.
|
2024-08-27 |
|
ucsc-fasize
|
public |
print total base count in fa files.
|
2024-08-27 |
|
ucsc-pslfilter
|
public |
filter out psl file
|
2024-08-27 |
|
ucsc-farandomize
|
public |
Program to create random fasta records
|
2024-08-27 |
|
ucsc-bigbedsummary
|
public |
Extract summary information from a bigBed file.
|
2024-08-27 |
|
ucsc-rmfadups
|
public |
remove duplicate records in FA file
|
2024-08-27 |
