I'm performing within-species blast searches on nucleotide data to identify gene regions that may be single-copy. I've produced an outfmt 6 output. It's clear that there are some gene regions that have hit other gene regions with high similarity, relatively low evalues, and moderate bit scores (compared to bit score from the gene aligning to itself). I would like to remove these "multiple-copy" sequences. I've seen other threads that have manage to extract single-hits, but when I have tried these scripts, it only removes the duplicate query ID entries (i.e., all by one of the gene regions hitting other gene regions are removed); I need them all removed.
Thanks!
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written
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mforthman •
1 answer
If I'm getting you right you want the query regions with only one hit (themselves). cut -f 2 outfile.out |sort |uniq -c | awk '$1==1' | grep -f - -w outfile.out I'm not sure about the awk part, maybe you need to play with it a bit (remove consecutive spaces or so), play with it.
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