convert knownGenes to fasta
Usage: kg2fa [options] Files
Options:
--coding
ignore non-coding transcripts.
Default: false
-D, --default
Use default Known Gene source from UCSC.
Default: false
--dict
Write optional dict file
--empty
Discard empty files.
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
--introns, --intron
Remove introns
Default: false
-o, --output
Output file. Optional . Default: stdout
* -r, -R, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard CreateSequenceDictionary
--case, --style
style: (0) do nothing (1): all UPPERCASE (2): all lowercase (3): exon
UPPERCASE + intron LOWERCASE . Otherwise do nothing
Default: 0
--utrs, --utr
Remove UTRs
Default: false
--version
print version and exit
-L
fasta line length.
Default: 50
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew kg2fa
The java jar file will be installed in the dist
directory.
2019-02-13
The project is licensed under the MIT license.
Should you cite kg2fa ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030