Who Can Give Me A Detailed Discription About The .Gp Format?

Question

[pengcui1989]

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?

Answer 1

[Sukhi Singh]

.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

[pengcui1989]

Oh, yes, this is what I want to find! Your detailed answer is very helpful! Thank you very much!