|
ucsc-twobitinfo
|
public |
get information about sequences in a .2bit file
|
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 |
|
fastani
|
public |
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
|
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 |
|
ucsc-parahub
|
public |
parasol hub server version 12.18
|
2024-08-27 |
|
ucsc-psltobigpsl
|
public |
converts psl to bigPsl input (bed format with extra fields)
|
2024-08-27 |
|
ucsc-faalign
|
public |
Align two fasta files
|
2024-08-27 |
|
ucsc-mafsinregion
|
public |
Extract MAFS in a genomic region
|
2024-08-27 |
|
ucsc-hgloadchain
|
public |
Load a generic Chain file into database
|
2024-08-27 |
|
ucsc-bedextendranges
|
public |
extend length of entries in bed 6+ data to be at least the given length,
|
2024-08-27 |
|
ucsc-dbtrash
|
public |
drop tables from a database older than specified N hours
|
2024-08-27 |
|
ucsc-genepredtofakepsl
|
public |
Create a psl of fake-mRNA aligned to gene-preds from a file or table.
|
2024-08-27 |
|
ucsc-newprog
|
public |
make a new C source skeleton.
|
2024-08-27 |
|
ucsc-pslstats
|
public |
collect statistics from a psl file.
|
2024-08-27 |
|
ucsc-hgfindspec
|
public |
Create hgFindSpec table from trackDb.ra files.
|
2024-08-27 |
|
ucsc-gtftogenepred
|
public |
convert a GTF file to a genePred
|
2024-08-27 |
|
ucsc-maskoutfa
|
public |
Produce a masked .fa file given an unmasked .fa and
|
2024-08-27 |
|
ucsc-taillines
|
public |
add tail to each line of file
|
2024-08-27 |
|
ucsc-bedgraphtobigwig
|
public |
Convert a bedGraph file to bigWig format.
|
2024-08-27 |
|
ucsc-bigwigmerge
|
public |
Merge together multiple bigWigs into a single output bedGraph.
|
2024-08-27 |
