For technical reason one set of reads is sequences to 100bp, and another set of reads from the same pair is sequences at 80 bp (that is, in the same pair one read is 80 bp and another one is 100 bp). Is it a problem if I just start mapping them with Bowtie as they are, or additional manipulations are needed?
PS. I tried mapping wing Bowtie without trimming and it gives 0 mapped reads so far.
What is the way to process an unmapped fastq file to have both files sequenced 80 bp?