I have a question pertaining to the trimming of custom/staggered adapter sequence in a FASTQ file.
I have a library with 4 different adapter lengths on the 5' side; this was done to increase library diversity during sequencing. However now I want to trim off the adapter and I can't do it by length!
Here's the 4 potential adapter sequence:
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCGGGGACTTATCAGCCAACC AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNCGGGGACTTATCAGCCAACC AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNCGGGGACTTATCAGCCAACC AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNCGGGGACTTATCAGCCAACC
And now I would like to trim off all "CGGGGACTTATCAGCCAACC" (and everything upstream!) from my reads - does anyone know how I can do it?
Thanks a lot for any help! Please let me know if further information is needed.