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PierreBSC / Viral-Track

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How to get gene expression of Virus? #8

Closed Dragonlongzhilin closed 4 years ago

Dragonlongzhilin commented 4 years ago

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? 图片1

PierreBSC commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

@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 commented 4 years ago

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