Dear SunYoung, 1)Here is info about the GTF format: http://genome.ucsc.edu/FAQ/FAQformat.html#format4
The GTF format is based off of the GFF format: http://genome.ucsc.edu/FAQ/FAQformat.html#format4 In order to get the additional fields that you are interested in, you will need to to change the "output format:" in the table browser to: "selected fields from primary and related tables" Click "get output" Click on the desired fields that you would like to have in your output. Click "get output" 2) Here is information on what chrN_random means: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download10 Hopefully this helps! If you have further questions, please contact the mailing list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "sylee" <[email protected]> To: [email protected] Sent: Wednesday, January 26, 2011 5:51:42 PM Subject: [Genome] problem: GTF file from UCSC Table. Dear Sir/Ma'am Hi, I downloaded current version of Mus_musculus GTF file from UCSC Tables. However I have the following problem. 1. If I select 'Ensembl Genes' track, the schema for Ensembl Genes has 'name2'(Gene symbol) column. But, when I select GTF output format, GTF file doesn't have [gene name2] column, it has only gene_id(Ens ID) and transcript_id in Attribute column. like this: chr1 mm9_ensGene CDS 134222783 134222806 0.000000 + 2 gene_id "ENSMUST00000072177"; transcript_id "ENSMUST00000072177"; And, when I select 'RefSeq Genes' track and GTF output format, this GTF file doesn't have name column(NM_number). Could you let me know how I can get the name2(gene symbol) or refSeq 'NM_number' in GTF file? 2. when I open GTF file, I can see 'chr1_random'. what does the random mean? because of 'chr*_random', I got the error message from other many analysis programs. I don't want to exclude the whole chr*_random. Best regards, Sincerely from SunYoung. ----------------------------------------------------- Sun-Young Lee Laboratory of Genomics & Genomic Medicine Lee Gil Ya Cancer and Diabetes Institute Gachon University of Medicine and Science Tel : +82 32 899 6545 Fax : +82 32 899 6519 Mobile : +82 19 278 0920 e-mail: [email protected]; [email protected] ----------------------------------------------------- _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
