I would like to ask for recommendations/workflows on how to asses the results of our de-novo assembly from a trinity run.
We have done a Trinity run and got a
transcripts.fasta files with the assembled transcripts.
Now we would like to compare these transcripts to an annotated genome of a close relative (which has a gtf file) to try and answer two questions.
- To asses the quality of our trinity output for completeness and correctness.
- To try and identify functionality of our newly assembled transcript via sequence homology.
I would appreciate some suggestions as to how to do both of these assignments.