I have paired-end data (in two separate files). I have groomed my files, and would like to filter the reads for quality. However, the read lengths for some of the paired reads are not equal. If I filter the files independently, the mapping fails as the two files contain different numbers of reads. If I use FASTQ Joiner to merge the data, then filter, I cannot use FASTQ Splitter as some reads (~44%) can't be split due to unequal read lengths. Any help gratefully received. For example, is there a way to trim reads so that the paired reads are the same length? I should say that I am a Galaxy newcomer, so go easy...!
What mapper are you using? Is the data Illumina? That has been previously manipulated to produce variable length reads?
Fastq files can be filtered so that both the forward and reverse inputs contain the same exact reads, but this is usually not necessary at the mapping step.