How to get gene symbol - Githubissues

PierreBSC / Viral-Track

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How to get gene symbol #6

Closed weichen123hahah closed 4 years ago

weichen123hahah commented 4 years ago

I have run the script Viral_Track_cell_demultiplexing.R' ,and get the file 'Expression_table.tsv',but don't have gene symbol in row just like 'refseq|NC_009334|172764nt|Human.3' or 'GL000224.1.2' in assembly GTF and 'RPMS1,A73' in my own GTF ,so how to get the gene symbol like EBNA-1,or how to creat a correct gtf file.Thanks!

PierreBSC commented 4 years ago

Hi there,

Sorry for the delay ! Indeed by default the quantification is done by using the GTF produced by StringTie... The use of a provided GTF is not possible yet and will be implemented only later.. One possibility is that you manually replaced the computed GTF file by a provided one and then relaunch the Viral_Track_cell_demultiplexing script. Just take care to replace the scaffold name of HSV-4 by refseq|NC_009334|172764nt|Human.3 !

Best

Pierre