I am relatively new to RNA-seq, and have some question about the HiSeq 2000 RNA-seq 100bp pair-end data.
I got the data from the lab next door, and I did some quality control with fastqc.
the reads quality look fine: http://postimg.org/image/ifu6jq8wr/
but the per base content looks wrong at the first several 30 bases http://postimg.org/image/ybke367gz/
and there are a lot of duplicate reads http://postimg.org/image/t4530u5zz/
what's wrong with the sequencing?
Do the reads still have adapters that I need to trim off?