counts of transcripts

[pw noyce]

I have pacbio RNA seq from the isoseq 3 pipeline. I do not have a reference genome or a reference trnascriptome. Can corset give me a matrix of transcript counts (samples as columns and non redundant transcipts as rows)

[Nadia Davidson]

Hi,

Corset will cluster the reads into gene group and output two files: one with counts (samples as columns and cluster ID as rows), the second is a list of which reads belong to each cluster. So it's really designed for gene-level analysis rather than transcript-level. For transcripts-level you could try something like running corset to get the "genes", then run Lace (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1284-1 https://github.com/Oshlack/Lace/wiki), or look for a long read de novo assembly, such as RATTLE.

Cheers,

Nadia.