Good Afternoon Allissa:
Please note the discussion of the "file" argument in the usage message
in place of where you would have the "database" argument on the command line.
You can also add this three line file to $HOME/.hg.conf:
db.host=genome-mysql.cse.ucsc.edu
db.user=genomep
db.password=password
To use the UCSC database to extract gene models from UCSC tracks.
--Hiram
Dillman, Allissa (NIH/NIA/IRP) [F] wrote:
>
> I am trying to run the genepredtogtf with my own file as the database but it
> still gives me the error that it cannot open the /home/dillmana/.hg.conf , no
> such file or directory. I don't need it to call the ucsc database, so I am
> not sure why it is giving me this error.
> This is the command: genePredToGtf
> /data/dillmana/macaque_index/macaque_index /data/dillmana/GRCh37toMq.txt
> /data/dillmana/humantomacaque.gtf
genePredToGtf - Convert genePred table or file to gtf.
usage:
genePredToGtf database genePredTable output.gtf
If database is 'file' then track is interpreted as a file
rather than a table in database.
options:
-utr - Add 5UTR and 3UTR features
-honorCdsStat - use cdsStartStat/cdsEndStat when defining start/end
codon records
-source=src set source name to uses
-addComments - Add comments before each set of transcript records.
allows for easier visual inspection
Note: use a refFlat table or extended genePred table or file to include
the gene_name attribute in the output. This will not work with a refFlat
table dump file. If you are using a genePred file that starts with a numeric
bin column, drop it using the UNIX cut command:
cut -f 2- in.gp | genePredToGtf file stdin out.gp
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