I have untrimmed Fastq files from RNA seq. I do a FastQC analysis and it shows me errors : Per base sequence content = FAIL
Per sequence GC content = !
Sequence Length Distribution = !
Sequence Duplication Levels = !
I have tried using cutadapt and Trim Galore to trim the files but in both the situations the software returns files with 0% trimming of adapters. The software is identifying the adapters as I can see that in the result files, but it is not rimming the adapters or the poly a tail.
I have just started using Galaxy and therefore, I do not understand how to put in more stringent conditions for trimming. The libraries were made using Lexogen Quant seq kit and they have a poly a tail.