I have a somewhat difficult problem to find a solution to on google. I need to trim my fastq files up until a sequence, and not remove that sequence (but remove everything before it).
This someRandomNoise_aKnownSequence_unknownSequence becomes aKnownSequence_unknownSequence
All the tools I use, and that I have seen, would remove both the "someRandomNoise" and the "aKnownSequence"
I could try to find the location of the sequence in each read and then trim then in a loop, but this seem very inefficient.