Hi, I have a genome in two fastq files, an I have tried to determinate the deep coverage using, bwa, samtools, and BAMstats, the problem is that some sequences in R1 file are empty but they could be not in R2, as well some of them in R2 are empty but not in R1, that make some errors in bwa. So I want to keep the same reads (same number of reads, same order, and the same names in both files) that are not empty in both files..... any suggestion ??? I have tried to make a perl script, but I just can't find the way to fix it..... Any Software to fix that problem ???
Thanks So Much !!