grep pattern in both start and end, but with mismatch in the middle of sequence
Hi everyone
I'm looking for a method to perform grep in both start and end of a sequencing, but allowing one, two or three mismatch in the middle.
[conservative match] + match with maximum of three mismatch + [conservative match]
I tried grep from seqkit, but this tool allow mismatch in the entire sequence.
Best regards, Willian
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This may be what you are looking for: https://unix.stackexchange.com/questions/163726/limit-grep-context-to-n-characters-on-line
If these are fastq files then some creative combination of
restrictright=andrestrictleft=may work withbbduk.shin filter mode. A guide is available here: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/