How to get gene expression of Virus?

[Dragonlongzhilin]

The expression result file, Expression_table.tsv, is included expression level of viral transcripts. If I want to use expression level of viral gene to analysis, what should I do?

[PierreBSC]

Hi,

Those are indeed viral 'genes' that have been detected by stringtie. Hovewer, in the case of SARS-CoV-2 this does not really make sense, as all reads will fall in the 3' end of the genome due to the transcription/replication process of this virus (nested transcription specific to Nidoviruses).

Hope this will help.

Best

Pierre

[Dragonlongzhilin]

Thank you for your prompt reply! In this case, could we directly sum these items as an 'gene' expression of SARS-CoV-2? If not, what should we do?

[sfortma2]

@Dragonlongzhilin For the count matrix you show in your original post, did you merge the Viral-Tracker expression_table.tsv with the count matrix created from another program? I'm only getting viral genes in my expression_table.tsv file

[Dragonlongzhilin]

@sfortma2 No，it just expression_table.tsv file provided by Virtal-Tracker.