I've got a data sample consisting of two mate-paired FASTQ files. I've applied paired-end Trimmomatic on both these FASTQ files and retrieved a
forward_accepted.fq and a
reverse_accepted.fq. Now I applied Bowtie2 to align both FASTQ files in forward-reverse order, and it seems like there seems to be inconsistency in the amount of reads of the
forward_accepted.fq and the
Is there some easy way to fix this, such as a picard/gatk/samtools command that is able to delete the incorrect read pairs, or continue with the correct read pairs? Best solution for me would be input of 2 incorrect FASTQ files, and output of 2 correct FASTQ files.