How To Retrieve Results From A Blastx Ouput File (Pairwise)

Question

[rocpengliu]

Hi, guys

I am a novice in bioinformatics. Any ideas about how to retrieve the results from a blastx output file (pairwise)? For example, I got a 10,000 transcripts in a fasta file from a trinity assembly; those 10,000 transcripts were used to do blastx and i got the blastx output file (pairwise format). The question is that I only want to retrieve the first 5,000 transcripts's blastx results. How can i do that?

Answer 1

[Pappu]

Set option in blast to output results in tabular format. Then it will be very easy to parse using Python or other programming language.