My question is that my original data or pair end read data are consisted of Read1 and Read2 and they are corresponding to each other. When I have done quality filtering, Read1 and Read2 data are not corresponding to each other, is that mean my data are not pair-end data anymore? Is this the reason that BWA was failed when I assigned Read1 and Read2 read as pair end reads? If yes, I need to set them as single end read and run BWA "aln" separately, right? Last question is should I merge the read 1 BAM file and read2 BAM file together by using BWA "sampe"?
Thank you very much for the answer!!