|
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 |
|
ucsc-pslmap
|
public |
map PSLs alignments to new targets using alignments of
|
2024-08-27 |
|
ucsc-sqltoxml
|
public |
dump out all or part of a relational database to XML, guided
|
2024-08-27 |
|
ucsc-subcolumn
|
public |
Substitute one column in a tab-separated file.
|
2024-08-27 |
|
ucsc-hgloadmaf
|
public |
Load a maf file index into the database
|
2024-08-27 |
|
ucsc-chromgraphfrombin
|
public |
Convert chromGraph binary to ascii format.
|
2024-08-27 |
|
ucsc-genepredtobed
|
public |
Convert from genePred to bed format. Does not yet handle genePredExt
|
2024-08-27 |
|
ucsc-ixixx
|
public |
Create indices for simple line-oriented file of format
|
2024-08-27 |
|
ucsc-bedclip
|
public |
Remove lines from bed file that refer to off-chromosome locations.
|
2024-08-27 |
|
ucsc-ldhggene
|
public |
load database with gene predictions from a gff file.
|
2024-08-27 |
|
ucsc-mafspecieslist
|
public |
Scan maf and output all species used in it.
|
2024-08-27 |
|
ucsc-mafcoverage
|
public |
Analyse coverage by maf files - chromosome by
|
2024-08-27 |
|
ucsc-parasol
|
public |
Parasol is the name given to the overall system for managing jobs on a computer cluster and to this specific command. This command is intended primarily for system administrators. The 'para' command is the primary command for users.
|
2024-08-27 |
|
ucsc-mrnatogene
|
public |
convert PSL alignments of mRNAs to gene annotations
|
2024-08-27 |
|
ucsc-mafgene
|
public |
output protein alignments using maf and genePred
|
2024-08-27 |
|
ucsc-netfilter
|
public |
Filter out parts of net. What passes
|
2024-08-27 |
|
ucsc-hgloadnet
|
public |
Load a generic net file into database
|
2024-08-27 |
|
ucsc-toupper
|
public |
Convert lower case to upper case in file. Leave other chars alone
|
2024-08-27 |
|
ucsc-genepredcheck
|
public |
validate genePred files or tables
|
2024-08-27 |
|
ucsc-genepredfilter
|
public |
filter a genePred file
|
2024-08-27 |
|
ucsc-beditemoverlapcount
|
public |
count number of times a base is overlapped by the
|
2024-08-27 |
|
ucsc-pslmrnacover
|
public |
Make histogram of coverage percentage of mRNA in psl.
|
2024-08-27 |
|
ngs-bits
|
public |
Short-read sequencing tools
|
2024-08-27 |
|
minimap2
|
public |
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
|
2024-08-27 |
