Identifying and quantifying transcript variants in RNA-seq data

Question

[MieszkoL]

Hi,

I've processed FASTQ files with nf-core/rnaseq pipeline (GRCh38, hisat2 aligner, StringTie transcript assembly & quantification). After DEG & GSEA analysis, I'm interested in looking into transcript variants. Specifically, I want to look for truncated MDK transcript (if present) - https://www.ncbi.nlm.nih.gov/nuccore/DQ323888.1 . How do I do that? I'd really appreciate for pointing me in the right direction, which tools to use etc. Is stringtie --merge followed by gffcompare a good way to do it in this case?

Thank you! Mieszko

[benformatics]

try using one of the pseudo-aligners (kallisto/salmon) https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04198-1

Otherwise you need to try like DEXseq or something and recreate your "isoforms" manually

[MieszkoL]

If I'm understanding correctly, salmon/kallisto approach is limited by transcriptome used for annotation. Linked MDK transcript (DQ323888.1) is not in GRCh38.p13 and therefore it can't be detected this way, right?