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UCSC-LoweLab / tRAX

tRNA Analysis of eXpression
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dataframe used to do the differential expression analysis #24

Open lilia0610 opened 3 months ago

lilia0610 commented 3 months ago

Hi,

I am a newer in small RNA analysis and I have run the analysis with the pipeline successfully according to your instruction.

But considering the output, I have a doubt about the differential expression analysis, the dataframe used for differential expression analysis of tRNA by Deseq2 is the raw count of all annotated small RNA referred to git files or only annotated tRNA population? I think the dataframe chosen will effect the size factor to compare between group by differential expression analysis. Because the aligned reads of my each library is quite different.

Thanks!

alba1735 commented 3 months ago

Hello,

When running tRAX it uses all small RNA annotated data to determine Deseq2 normalization. However the small RNA data is comprised of the tRNAs found in your sequencing data (based on the tRNA database given “—databasename") and all RNAs found in the provided gtf with “—ensemblgtf". If you ONLY want to do normalization on tRNAs then for the “—ensemblgtf" flag just create an empty text file and call it “empty.gtf” and use that. It will no longer identify small RNAs and only tRNAs.