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.
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written
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sdbaney •
2 answers
The first part looks like a job for bedtools getfasta.
Love the comments xD
wild reading this in the AI era as a finishing phd student rip
- Pull only the transcripts listed in the gtf file from the FASTA file
Use bedtools getfasta.
- Find the longest ORFs
See this related thread for some options.
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