I have some Illumina RNA seq data, 75bp paired end reads. I've run FastQC & trimmomatic and then re-run FastQC. Both before and after trimmomatic quite a few of my sequences fail the per base sequence content with the %A content running low in read 1 (e.g. http://i.imgur.com/Cv4HXJq.png) and the %T running low in read 2 (e.g. http://i.imgur.com/ul7v55H.png). Read 2 tends to be a warning rather than a fail.
Per base quality is good across the board, per sequence GC content looks fine and the only other fails I get are duplicated sequences and kmer content (both of which I gather are common fails in mRNA seq data).
I've little experience with RNA seq QC - is this something to be concerned about?
Thanks for any advice.