Any tips on what to do downstream of a novel transcriptome assembly? I have a few things going based mainly on someone else in my group's previous work:
- basic stats about the contigs, length, etc.
- check for redundancy in contigs
- tabulate read counts per contig / create igv tracks
- examine coding potential of contigs
- blast against nr (or some subset?) to annotate contigs
I wanted to see if there are any additional things I should be doing. I assembled using trinity, the data is paired-end illumina sequences. I have one sample at this point.
I kind of liked this idea from seqanswers.