Hi everyone! please help me, I am new in this field, I have question in mapping and counting!
I was mapping an mouse RNA-seq data to genome (mm10) using STAR, to save time, I did not build STAR index by myself but use the mm10 genome index built by my colleague, and then I use the genome gtf file downloaded from hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/genes/mm10.knownGene.gtf, to do counting, the gtf file seems to be in ensembl ID.
However, in the counting result, the gene ID seems to be uniprot ID, not ensembl ID nor gene symbol, I guess if I have done any procedure wrong? If not, how can I get gene symbol from the ID?
Here is some information:
chr1 knownGene transcript 3073253 3074322 . + . gene_id "ENSMUST00000193812.1"; transcript_id "ENSMUST00000193812.1";
chr1 knownGene exon 3073253 3074322 . + . gene_id "ENSMUST00000193812.1"; transcript_id "ENSMUST00000193812.1"; exon_number "1"; exon_id "ENSMUST00000193812.1.1";
chr1 knownGene transcript 3102016 3102125 . + . gene_id "ENSMUST00000082908.1"; transcript_id "ENSMUST00000082908.1";
Please help me!