Hi,
I found there were huge difference in alignment by strand in my paired-end DNA sequence data. The samples were sequenced using Miseq. Each read is about 220bp long and my target gene is about 240bp long. So there are overlaps between a pair.
For example, given 17500 reads, for forward reads 808 are mapped while in the reverse case 16447 are mapped. I used BWA for the alignment. The situation is quite consistent in all my samples: always the forward reads are poorly mapped.
Does anyone have an explanation?
Many thanks
I found there were huge difference in alignment by strand in my paired-end DNA sequence data. The samples were sequenced using Miseq. Each read is about 220bp long and my target gene is about 240bp long. So there are overlaps between a pair.
For example, given 17500 reads, for forward reads 808 are mapped while in the reverse case 16447 are mapped. I used BWA for the alignment. The situation is quite consistent in all my samples: always the forward reads are poorly mapped.
Does anyone have an explanation?
Many thanks