I have forward and reverse fastq files, read names like below:
@SRR12477619.23832.1 1 length=150(forward)
@SRR12477619.23832.2 1 length=150(reverse)
It works when I run kneaddata version 0.7.2, and the same amount of reads are produced in the final paired 1 and 2 fastq files. However, when I run with the latest version of 0.10.0, there is no reads in the final paired 1 and 2 fastq files. May I ask the reason?
In addition, if I run with version 0.7.2, as the reads order in each fastq (1 and 2) are not same, can I use repair.sh from BBMap to sort them in the same order as required by assembler, such as MEGAHIT?