I am trying to remove low quality bases and 'N's from fastq sequence file. Now being a beginner perl programmer I do know how to handle fasta file, but not good enough with fastq, so I can only remove the base but not its quality value. Basically I am unable to form the logic on how to do it.
@FCC4WLAACXX:3:1101:1697:1896#GCCAATAT/1 NTCGAGGACCTTGGTTGAGCC + BP\ccceegggggiiiiiiih
Say I remove N in the beginning, then how do I remove the B (quality value) too?
Can anybody help me with this ?? A perl solution would be highly helpful. Thanks in advance, appreciate your time.