Hi, I have a de novo assembled FASTA file that I used with Cuffdiff. I now have a sorted gtf file (only retained the transcripts that were significantly differentially expressed).
Is there a program that I can use to: 1. pull only the transcripts listed in the gtf file from the FASTA file 2. find the longest ORFs
so that I can run some manual BLAST searches to validate my semi-automatic BLAST.
Is there an easy way to do this? Perhaps I just need to run a search function in the FASTA file using the transcript IDs listed in my sorted gtf file.