I'm working on a somewhat unusual transcriptome focused on a killer X chromosome. This chromosome has some new genes, with expression levels quite different from their autosomal paralogs.
I've found that Trinity does an ok job of assembling the distinct genes, but when I try to do a gene-level DE analysis, it lumps the distinct genes together. So, I lose important information by doing a gene-level DE analysis and need to use a transcript-level approach.
I've done blastx with all of my transcripts using diamond, and want to extract the isoform from each gene with the best score (bitscore). I'm trying to write a script to parse this, but my scripting skills aren't up to the task. Does anyone know of (or have) a script that can do this?