I have 2 sets of paired end sequencing files:
set1_r1.fastq and set1_r2.fastq for set 1
set2_r1.fastq and set2_r2.fastq for set 2.
The files in set 2 are considerably larger than the files in set 1.
I want to align the reads in set1 to set2 or at least determine the number of how many reads in set 1 align to set 2.
How can I best do this?
I understand that bowtie allows for aligning to an indexed reference genome. But here I want to align paired end fastq files to another set of paired end fastq files. Would it be possible to align both sets individually to the same reference genome and then somehow compare the output sam/bam files?
Is there any tool that can help me accomplish this?