Hello everyone!
I’m doing a quality analysis of my samples before we proceed to sequence my other samples.
My experiments are RNAseq 150bp paired-end 100M reads target (we accept up to a minimum of 30M good reads) with TruSeq Total RNA illumina kit, for FFPE samples (which are low quality)
When I try FastQC on aligned and trimmed samples, everything is fine, except for two things:
Per base sequence
This ones seems ok even if it failed. Seens like the distribution is ok, except in the very beggining of the k-mers
Per sequence GC content
This one is very weird. It looks like two peaks, which indicates rRNA contamination.
I would like to know if this seems like the case, and if so, how can I detect rRNA contamination and exclude it within galaxy?