Dear all, I know that we can download the GENCODE gene annotation information in a GTF format. Howerer, when I download the GENCODE gene annotion information in UCSC genome browser, I find that it is in .gp format. And the UCSC hasn't given detailed information about the .gp format. So who can give me detailed information about the .gp format? And how can I convert the .gp to GTF format?
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pengcui1989 •
.gp is the GenePred format . It looks like
PGOHUM00000244554 chr1 + 131124 135623 135623 135623 1 131124, 135623,
PGOHUM00000262410 chr1 - 228318 228773 228773 228773 1 228318, 228773,
PGOHUM00000251104 chr1 + 321107 326849 326849 326849 1 321107, 326849,
PGOHUM00000262420 chr1 + 327455 328172 328172 328172 1 327455, 328172,
PGOHUM00000259441 chr1 - 329365 329766 329766 329766 1 329365, 329766,
PGOHUM00000243866 chr1 - 379071 379468 379468 379468 1 379071, 379468,
Read more info here on the IGV page
The genePred table formats can be used to specify the gene track annotations for an imported genome. Several variations of the genePred table format are described in the FAQ titled “genePred table format” on the UCSC Genome Browser web site: http://genome.ucsc.edu/FAQ/FAQformat#format9. Downloading gene information from any of these tables creates a tab-delimited text file where the columns in the file match the columns in the table. Downloaded files may be zipped with a .txt.gz extension. Such a zipped file can be used to specify the gene track annotations for an imported genome.
Also for second question of yours, use genePredtoGtf from the kent resource and read more about it here.
I hope all this info will be quite detailed.
Cheers
Oh, yes, this is what I want to find! Your detailed answer is very helpful! Thank you very much!
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