|
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-hgfakeagp
|
public |
Create fake AGP file by looking at N's
|
2024-08-27 |
|
ucsc-paranode
|
public |
version 12.18
|
2024-08-27 |
|
ucsc-pslpretty
|
public |
Convert PSL to human-readable output
|
2024-08-27 |
|
ucsc-xmltosql
|
public |
Convert XML dump into a fairly normalized relational database
|
2024-08-27 |
|
ucsc-fafilter
|
public |
Filter fa records, selecting ones that match the specified conditions
|
2024-08-27 |
|
ucsc-chainswap
|
public |
Swap target and query in chain
|
2024-08-27 |
|
ucsc-ameme
|
public |
find common patterns in DNA
|
2024-08-27 |
|
ucsc-rowstocols
|
public |
Convert rows to columns and vice versa in a text file.
|
2024-08-27 |
|
ucsc-liftup
|
public |
change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf
|
2024-08-27 |
|
ucsc-crtreesearchbed
|
public |
Search a crTree indexed bed file and print all items that overlap query.
|
2024-08-27 |
|
ucsc-fatrans
|
public |
Translate DNA .fa file to peptide
|
2024-08-27 |
|
ucsc-localtime
|
public |
convert unix timestamp to date string
|
2024-08-27 |
|
ucsc-positionaltblcheck
|
public |
check that positional tables are sorted
|
2024-08-27 |
|
ucsc-bigpsltopsl
|
public |
convert bigPsl file to psl
|
2024-08-27 |
|
ucsc-pslrc
|
public |
reverse-complement psl
|
2024-08-27 |
|
ucsc-qactowig
|
public |
convert from compressed quality score format to wiggle format.
|
2024-08-27 |
|
ucsc-checkagpandfa
|
public |
takes a .agp file and .fa file and ensures that they are in synch
|
2024-08-27 |
|
ucsc-overlapselect
|
public |
Select records based on overlapping chromosome ranges. The ranges are specified in the selectFile, with each block specifying a range. Records are copied from the inFile to outFile based on the selection criteria. Selection is based on blocks or exons rather than entire range.
|
2024-08-27 |
|
ucsc-pslpostarget
|
public |
flip psl strands so target is positive and implicit
|
2024-08-27 |
|
ucsc-avecols
|
public |
average together columns
|
2024-08-27 |
|
ucsc-bedpileups
|
public |
Find (exact) overlaps if any in bed input
|
2024-08-27 |
|
ucsc-bamtopsl
|
public |
Convert a bam file to a psl and optionally also a fasta file that contains the reads.
|
2024-08-27 |
|
ucsc-netchainsubset
|
public |
Create chain file with subset of chains that appear in the net
|
2024-08-27 |
|
ucsc-splitfilebycolumn
|
public |
Split text input into files named by column value
|
2024-08-27 |
|
ucsc-paratestjob
|
public |
version 12.18
|
2024-08-27 |
|
ucsc-bigwiginfo
|
public |
Print out information about bigWig file.
|
2024-08-27 |
|
ucsc-bigwigcat
|
public |
merge non-overlapping bigWig files
|
2024-08-27 |
|
ucsc-bigwigaverageoverbed
|
public |
Compute average score of big wig over each bed, which may have introns.
|
2024-08-27 |
|
ucsc-maketablelist
|
public |
create/recreate tableList tables (cache of SHOW TABLES and DESCRIBE)
|
2024-08-27 |
|
ucsc-axttopsl
|
public |
Convert axt to psl format
|
2024-08-27 |
|
ucsc-tdbquery
|
public |
Query the trackDb system using SQL syntax.
|
2024-08-27 |
|
ucsc-bigwigtowig
|
public |
Convert bigWig to wig. This will keep more of the same structure of the
|
2024-08-27 |
|
ucsc-parasync
|
public |
uses paraFetch to recursively mirror url to given path
|
2024-08-27 |
|
ucsc-lavtopsl
|
public |
Convert blastz lav to psl format
|
2024-08-27 |
