|
ucsc-pslxtofa
|
public |
convert pslx (with sequence) to fasta file
|
2024-08-27 |
|
ucsc-bedcommonregions
|
public |
Create a bed file (just bed3) that contains the regions common to all inputs.
|
2024-08-27 |
|
ucsc-bedweedoverlapping
|
public |
Filter out beds that overlap a 'weed.bed' file.
|
2024-08-27 |
|
ucsc-chaintoaxt
|
public |
Convert from chain to axt file
|
2024-08-27 |
|
ucsc-bigbedtobed
|
public |
Convert from bigBed to ascii bed format.
|
2024-08-27 |
|
ucsc-hgloadsqltab
|
public |
Load table into database from SQL and text files.
|
2024-08-27 |
|
ucsc-axtswap
|
public |
Swap source and query in an axt file
|
2024-08-27 |
|
ucsc-ratolines
|
public |
Output .ra file stanzas as single lines, with pipe-separated fields.
|
2024-08-27 |
|
ucsc-pslselect
|
public |
select records from a PSL file.
|
2024-08-27 |
|
ucsc-axttomaf
|
public |
Convert from axt to maf format
|
2024-08-27 |
|
ucsc-autoxml
|
public |
Generate structures code and parser for XML file from DTD-like spec
|
2024-08-27 |
|
ucsc-pslliftsubrangeblat
|
public |
lift PSLs from blat subrange alignments
|
2024-08-27 |
|
ucsc-qactoqa
|
public |
convert from compressed to uncompressed
|
2024-08-27 |
|
ucsc-bigwigcluster
|
public |
Cluster bigWigs using a hacTree
|
2024-08-27 |
|
ucsc-ticktodate
|
public |
Convert seconds since 1970 to time and date
|
2024-08-27 |
|
ucsc-chainantirepeat
|
public |
Get rid of chains that are primarily the results of repeats and degenerate DNA
|
2024-08-27 |
|
ucsc-headrest
|
public |
Return all *but* the first N lines of a file.
|
2024-08-27 |
|
ucsc-pslswap
|
public |
Swap target and query in psls
|
2024-08-27 |
|
ucsc-qacagplift
|
public |
Use AGP to combine per-scaffold qac into per-chrom qac.
|
2024-08-27 |
|
ucsc-chainmergesort
|
public |
Combine sorted files into larger sorted file
|
2024-08-27 |
|
ucsc-tolower
|
public |
Convert upper case to lower case in file. Leave other chars alone
|
2024-08-27 |
|
ucsc-bigmaftomaf
|
public |
convert bigMaf to maf file
|
2024-08-27 |
|
ucsc-newpythonprog
|
public |
Make a skeleton for a new python program
|
2024-08-27 |
|
ucsc-chainstitchid
|
public |
Join chain fragments with the same chain ID into a single
|
2024-08-27 |
|
ucsc-genepredtobiggenepred
|
public |
converts genePred or genePredExt to bigGenePred input (bed format with extra fields)
|
2024-08-27 |
|
ucsc-gff3topsl
|
public |
convert a GFF3 CIGAR file to a PSL file
|
2024-08-27 |
|
ucsc-chaintopslbasic
|
public |
Basic conversion chain file to psl format
|
2024-08-27 |
|
ucsc-pslmappostchain
|
public |
Post genomic pslMap (TransMap) chaining. This takes transcripts that have been mapped via genomic chains adds back in blocks that didn't get include in genomic chains due to complex rearrangements or other issues.
|
2024-08-27 |
|
ucsc-facount
|
public |
count base statistics and CpGs in FA files.
|
2024-08-27 |
|
ucsc-bedsort
|
public |
Sort a .bed file by chrom,chromStart
|
2024-08-27 |
|
ucsc-fatofastq
|
public |
Convert fa to fastq format, just faking quality values.
|
2024-08-27 |
|
ucsc-nibsize
|
public |
print size of nibs
|
2024-08-27 |
|
ucsc-splitfile
|
public |
Split up a file
|
2024-08-27 |
|
ucsc-fastqstatsandsubsample
|
public |
Go through a fastq file doing sanity checks and collecting stats
|
2024-08-27 |
|
ucsc-maftopsl
|
public |
Convert maf to psl format
|
2024-08-27 |
|
ucsc-fatotab
|
public |
convert fa file to tab separated file
|
2024-08-27 |
|
ucsc-bedgraphpack
|
public |
Pack together adjacent records representing same value.
|
2024-08-27 |
|
ucsc-pslscore
|
public |
calculate web blat score from psl files
|
2024-08-27 |
|
ucsc-fafrag
|
public |
Extract a piece of DNA from a .fa file.
|
2024-08-27 |
|
ucsc-linestora
|
public |
generate .ra format from lines with pipe-separated fields
|
2024-08-27 |
|
ucsc-pslhisto
|
public |
Collect counts on PSL alignments for making histograms. These then be analyzed with R, textHistogram, etc.
|
2024-08-27 |
|
ucsc-countchars
|
public |
Count the number of occurrences of a particular char
|
2024-08-27 |
|
ucsc-psldropoverlap
|
public |
deletes all overlapping self alignments.
|
2024-08-27 |
|
ucsc-mafranges
|
public |
Extract ranges of target (or query) coverage from maf and
|
2024-08-27 |
|
ucsc-fasomerecords
|
public |
Extract multiple fa records
|
2024-08-27 |
|
ucsc-twobitmask
|
public |
apply masking to a .2bit file, creating a new .2bit file
|
2024-08-27 |
|
ucsc-lavtoaxt
|
public |
Convert blastz lav file to an axt file (which includes sequence)
|
2024-08-27 |
|
ucsc-twobittofa
|
public |
Convert all or part of .2bit file to fasta
|
2024-08-27 |
|
ucsc-hgfakeagp
|
public |
Create fake AGP file by looking at N's
|
2024-08-27 |
|
ucsc-paranode
|
public |
version 12.18
|
2024-08-27 |
