fqgrep #1
Description
--Hi,
I usually use the fqgrep tool (https://github.com/indraniel/fqgrep) for the search pattern in FASTA/FASTQ files.
Also, I use this command:
fqgrep -f -m 0 -d 0 -e -p '^[ARNDCQEGHILKMFPSTWYV_]{3,}C[ARNDCQEGHILKMFPSTWYV_]{31,35}C[ARNDCQEGHILKMFPSTWYV*]{3,}$' in > out
with:
-m Total number of mismatches to at most allow for in search pattern [Default: 0]
-d Max threshold of deletion mismatches to allow for in search pattern [Default: unlimited]
-e Force tre regexp engine usage
-p Pattern of interest to grep
I would be happy to compare my results with those returned by motex but I need help to properly configure it.
Can you help me?
Thank you so much.
Laurent --