We recently extracted RNA seq data from human stool samples. We got reads that are 75bp and 150bp. These are paired-end reads. These are aligned with BWA.
When we aligned 75bp we got less alignment for human genome but when we aligned 150bp we could see more alignment for the human genome. So my question why are we seeing more reads aligned to human genome with 150bp compared to 75bp? This is the first time we are working with microbial data, any suggestions are appreciable. Thanks in Advance, Hothri