I'm analyzing my first RNA-seq results that were obtained from a bacterial strain at two conditions: control vs. stress.
Because the bowtie2 mapping ratio of stress condition was much lower (57%) compared to control (86%), I looked into the FastQC results and also manually checked sequences.
This is the per sequence GC content plot of control condition. I think there is no problem, with a peak around the genomic GC content (52%).
But, the per sequence GC content of stress condition seems to be very abnormal. There is a very thick tail toward low GC.
Also, when I checked the sequences from the stress condition, I found that many sequences look very weird like below.
Note that the above plots and sequences were obtained after trimming (by bbduk).
What might go wrong in the stress condition?