This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Abundance Counting for Non-Model Organism for edgeR

I am working with a non-model organism (no annotated genome or the option to use an annotation file in my abundance counting). I performed de novo transcriptome assembly of the Illumina HiSeq4000 reads.

I originally used StringTie as my abundance counter because I didn't need a gtf annotation file and it created one I could use for the differential expression analysis but I am now seeing that because of its feature to predict isoforms, I am having trouble matching up their IDs with my assembly IDs (there being more stringtie IDs than assembly because of its novel prediction).

Is there any way to disable this feature in StringTie? Is there another program I can use to create a gtf file so that I can use featureCounts or just count abundances that will not require a gtf?

rna-seq abundance edger
• 1,489 views • link
updated by ATpoint ATpoint • written by sdbaney • sdbaney

1 answer

You can use salmon to quantify reads against a transcriptome in fasta format. From there on you can summarize transcript count to the gene level with tximport.

• 0 views • link
written by ATpoint ATpoint

Thank you, I think that’s what I’m going to end up doing. As stringtie seems to be causing more headache than anticipated.

• 0 views • link
written by sdbaney • sdbaney

Log in to answer this question.

More posts like this