I have .fastq files from the same sample sequenced in two sequencing runs.
First run was on Illumina Hiseq and generated paired-end 2x100bp reads. Second run was on Miseq and generated paired-end 2x250bp reads.
Can I just merge the .fastq files of both runs (using cat), keeping off course R1 and R2 separate and then align with BWA? Or are the different read lengths going to pose a problem?