gravatar for hellocita

2 hours ago by

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:

head mm10.knownGene.gtf

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";

head genes
A0A023T778
A0A075B5I2
A0A075B5J3
A0A075B5J4
A0A075B5K6
A0A075B5L1
A0A075B5L2
A0A075B5L3
A0A075B5L7
A0A075B5L8
A0A075B5M4
A0A075B5P0
A0A075B5P1
A0A075B5P4
A0A075B5P6
A0A075B5P8
A0A075B5P9
A0A075B5Q0

Please help me!

link

modified 2 hours ago

written
2 hours ago
by

hellocita20



Source link