Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
2
0
Entering edit mode
Bo • 0
@e0db819c
Last seen 10 weeks ago
United States

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

STAR tximport RNASeq DESeq2 • 795 views
ADD COMMENT
2
Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States

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.

0
Entering edit mode

Thanks! This is really helpful!

ADD REPLY
0
Entering edit mode
swbarnes2 ★ 1.3k
@swbarnes2-14086
Last seen 2 days ago
San Diego

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.

ADD COMMENT

Login before adding your answer.

Traffic: 457 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6