parsing cd-hit result
I have cluster sequences using cd-hit-est and now I want to filter out the parent or the representative sequence out of the cluster. Any suggestions?
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Joseph Hughes
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You can use the * symbol at the end of the line to pull out the representative sequence. I think that this script I wrote, will pull out the representative sequence: https://github.com/josephhughes/TCRclust/blob/master/sort_cdhit.pl
using:
sort-cdhit.pl -i INFILE.fa -o OUTFILE_rep.fa -clstr INFILE.clstr -rep
You will need to make sure you use the option -d 0 when you run cd-hit to be sure to get the complete identifier in the .clstr output file.
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Joseph Hughes
Yes. grep.
Read the user guide - it mentions a pattern you can use to isolate the representative sequences.
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