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
