Hi,

I am new to RNA-seq analysis. I have finished RNA alignment using STAR, and got ReadsPerGene.out.tab outputs. I am trying to use tximport to build a gene-level count matrix for DESeq2 analysis using the STAR outputs. Yet I haven't been able to find a way to do it. I have checked the vignettes for tximport and DESeq2.

I am wondering if anyone has suggestions on how to use tximport and STAR outputs to make a gene-level count matrix?

Thanks,

Bo

The short answer is that you don't. tximport is meant to summarize transcript abundance estimates at the gene level, and as you might imagine, ReadsPerGene.out.tab contains gene reads, not transcript. You could (probably) just read those data in directly, or use the conventional route of using e.g. Rsubread or GenomicAlignments to count the overlaps from your bam files. You can read the vignettes for those two packages if that's the way you want to go.

Use a little bit of R to pull the desired column from all the gene.result files to make one matrix. This matrix can be used for making the dds object.