I am using StringTie for transcript assembly and mRNA expression profiling. Now I have ballgown files with some .ctab and .gtf files. Now I want to use DESeq2 for differential expression analysis. But I cannot use .ctab and .gtf files directly to DESeq2. Could you all suggest to me how to use DESeq2 for differential expression analysis in this instance? Thank you,
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khanald2114 •
1 answer
StringTie abundance estimates can be imported into R for use with DESeq using tximport::tximport. You will need a table mapping transcripts IDs to geneIDs (I think) if you want to do gene level analysis. I don't know if this is in the ctab or whether you need to manually extract it from the GTF. You can then import the estaimted counts into a DESeq object using DESeq2::DESeqDatasetFromTximport.
Personally, if I need to do de novo transcript assembly, I assemble with StringTie, and the use the resultant GTF file to requantitate the fastq files using salmon.
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