Hi Recently we have prepared 3 paired end libraries (2X100) and sequenced on illumina hiseq 1000. we have checked the quality of the sequenced reads and found that for one library both forward and reverse reads showed good quality fatsQC reports. However for other 2 libraries the fastQC report for forward read (R1) is very good. But the fastQC report for reverse read is looking really bad (especially the per base quality score). I suppose if there is any problem with the library preparation then it should affect both the reads (R1, R2) which is not the case here.Could anyone let me know the reason why this is happening? I have posted this in seqanswers as well.