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.
A00718:140:HWK2FDSXX:3:1414:5059:20807 1:N:0:CCTATGCC+CAAGCTTA CAAAAAAAAAGAACAAGCAAAAGAACACAACAAAAAAAAAAAAAACAAAAAAAAAAAAACAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAT A00718:140:HWK2FDSXX:3:1561:21287:5572 1:N:0:CCTATGCC+CAAGCTTA GTTTTTTTTGTCTTTTGTGTTTTGTTGTGGTTGGTTTGCTTTGTTGTTTTTGTGGGTTGGTTGTTTTTTTTTTTGTTGTTTGTTTTTTTTTTTTTTTGGTT A00718:140:HWK2FDSXX:3:1436:24948:22310 1:N:0:CCTATGCC+CAAGCTTA CAGCACCACACAAGCAGACCCCTGCGCACAAACACGAAACCCACCCGCCCGGGCCCCCGCGCCCGCCGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGGGC A00718:140:HWK2FDSXX:3:1337:16532:12273 1:N:0:CCTATGCC+CAAGCTTA CACCAACAAAAAAAAACCAAAACACAAAAAACCAAAACCAAAAAACAAAAACAAAAAAAAAAAACCAAAAAAAAAAAAACAACAAAAAAACAAAAGAACAA
Note that the above plots and sequences were obtained after trimming (by bbduk).
What might go wrong in the stress condition?