What is the best way to generate a good comparison crunch file for ACT? The manual is not very helpful. I tried using WebACT but I do not get any output from it. MSPCrunch also did not work well. tblastx works well but the hits are fragmented. Do you know of any tblastx parameters that I can tweak to get more "broad" hits. Also, I want to compare two multi-FASTA files ( indexed by faidx) with associated gff files (indexed by tabix), so is it possible to create a similar indexed crunch file between them?

Abhinay Ramaprasad
PhD Candidate
Pathogen Genomics Laboratory (Dr. Arnab Pain)


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