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ucsc-maffrag
|
public |
Extract maf sequences for a region from database
|
2024-08-27 |
|
ucsc-maforder
|
public |
order components within a maf file
|
2024-08-27 |
|
ucsc-maftosnpbed
|
public |
finds SNPs in MAF and builds a bed with their functional consequence
|
2024-08-27 |
|
ucsc-genepredsinglecover
|
public |
create single-coverage genePred files
|
2024-08-27 |
|
ucsc-hgloadbed
|
public |
Load a generic bed file into database
|
2024-08-27 |
|
ucsc-bedtogenepred
|
public |
convert bed format files to genePred format
|
2024-08-27 |
|
ucsc-liftover
|
public |
Move annotations from one assembly to another
|
2024-08-27 |
|
ucsc-transmappsltogenepred
|
public |
convert PSL alignments of mRNAs to gene annotations.
|
2024-08-27 |
|
ucsc-featurebits
|
public |
Correlate tables via bitmap projections.
|
2024-08-27 |
|
ucsc-trfbig
|
public |
Mask tandem repeats on a big sequence file.
|
2024-08-27 |
|
ucsc-getrnapred
|
public |
Get virtual RNA for gene predictions
|
2024-08-27 |
|
ucsc-netclass
|
public |
Add classification info to net
|
2024-08-27 |
|
ucsc-bedintersect
|
public |
Intersect two bed files
|
2024-08-27 |
|
ucsc-qatoqac
|
public |
convert from uncompressed to compressed
|
2024-08-27 |
|
ucsc-findmotif
|
public |
find specified motif in sequence
|
2024-08-27 |
|
ucsc-faonerecord
|
public |
Extract a single record from a .FA file
|
2024-08-27 |
|
ucsc-checktablecoords
|
public |
check invariants on genomic coords in table(s).
|
2024-08-27 |
|
ucsc-getrna
|
public |
Get mrna for GenBank or RefSeq sequences found in a database
|
2024-08-27 |
|
ucsc-hgbbidblink
|
public |
Add table that just contains a pointer to a bbiFile to database. This program
|
2024-08-27 |
|
ucsc-ratotab
|
public |
Convert ra file to table.
|
2024-08-27 |
|
ucsc-pslpairs
|
public |
join paired ends in psl alignments
|
2024-08-27 |
|
ucsc-fapolyasizes
|
public |
get poly A sizes
|
2024-08-27 |
|
ucsc-maffrags
|
public |
Collect MAFs from regions specified in a 6 column bed file
|
2024-08-27 |
|
ucsc-facmp
|
public |
Compare two .fa files
|
2024-08-27 |
|
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-pslcdnafilter
|
public |
Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given cDNA and non-comparative, based only on the quality of an individual alignment.
|
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-stringify
|
public |
Convert file to C strings
|
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-wigtobigwig
|
public |
Convert ascii format wig file (in fixedStep, variableStep
|
2024-08-27 |
