I have sequence some plasmid DNA using Nanopore sequencing (whole plasmid was sequenced). I am only interested in one region, therefore I would like to extract from the fasta file (around 10000 reads) just 425 bp from a specified location in each 4600 bp read (i.e. everything after atgacccg to be kept, or delete everything before this sequence).
Would someone be as kind as to help me do this? I've tried a few tools, but they fail with the long nanopore reads.
Many thanks in advance