|
ucsc-genepredtofakepsl
|
public |
Create a psl of fake-mRNA aligned to gene-preds from a file or table.
|
2025-06-30 |
|
ucsc-checkcoveragegaps
|
public |
Check for biggest gap in coverage for a list of tracks.
|
2025-06-30 |
|
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.
|
2025-06-30 |
|
ucsc-mafspecieslist
|
public |
Scan maf and output all species used in it.
|
2025-06-30 |
|
ucsc-qacagplift
|
public |
Use AGP to combine per-scaffold qac into per-chrom qac.
|
2025-06-30 |
|
ucsc-countchars
|
public |
Count the number of occurrences of a particular char.
|
2025-06-30 |
|
ucsc-netsyntenic
|
public |
Add synteny info to net.
|
2025-06-30 |
|
ucsc-maftoaxt
|
public |
Convert from maf to axt format.
|
2025-06-30 |
|
ucsc-blasttopsl
|
public |
Convert blast alignments to PSLs.
|
2025-06-30 |
|
ucsc-bigwigcluster
|
public |
Cluster bigWigs using a hacTree.
|
2025-06-30 |
|
ucsc-genepredhisto
|
public |
Get data for generating histograms from a genePred file.
|
2025-06-30 |
|
ucsc-maforder
|
public |
Order components within a maf file.
|
2025-06-30 |
|
ucsc-farc
|
public |
Reverse complement a FA file.
|
2025-06-30 |
|
ucsc-rowstocols
|
public |
Convert rows to columns and vice versa in a text file.
|
2025-06-29 |
|
ucsc-localtime
|
public |
Convert unix timestamp to date string.
|
2025-06-29 |
|
ucsc-ratolines
|
public |
Output .ra file stanzas as single lines, with pipe-separated fields.
|
2025-06-29 |
|
ucsc-lavtopsl
|
public |
Convert blastz lav to psl format.
|
2025-06-29 |
|
ucsc-dbsnoop
|
public |
Produce an overview of a database.
|
2025-06-29 |
|
ucsc-maftosnpbed
|
public |
Finds SNPs in MAF and builds a bed with their functional consequence.
|
2025-06-29 |
|
ucsc-ratotab
|
public |
Convert ra file to table.
|
2025-06-29 |
|
ucsc-nettoaxt
|
public |
Convert net (and chain) to axt.
|
2025-06-29 |
|
ucsc-facmp
|
public |
Compare two .fa files.
|
2025-06-29 |
|
ucsc-tdbquery
|
public |
Query the trackDb system using SQL syntax.
|
2025-06-29 |
|
ucsc-maffrags
|
public |
Collect MAFs from regions specified in a 6 column bed file.
|
2025-06-29 |
|
ucsc-nibsize
|
public |
Print size of nibs.
|
2025-06-29 |
