I have to analyze differential expression on 2 SRA files containing data from a small RNA sequencing experiment (single-ended).
I converted those to .fastq files to control their quality using FastQC, and I get many warnings and errors:
- Error in Per base sequence content
- Warning in Per sequence GC content
- Error in Sequence Duplication Levels
- Error in Overrepresented Sequences: sooo many RNA PCR primers indexes (1, 43, 30, 7), and Illumina Small RNA adapter.
- Error in Adapter Content: it was expected, Illumina Small RNA 3' adapter.
I used the following line of code to trim the adapter:
trim_galore /root/SRR12737828_pass.fastq.gz /root/SRR12737830_pass.fastq.gz > report
It successfully removed the adaptor, but it looks like it truncated the primers sequence too! I also don't know how to get rid (and if I have to?) of the primers... Am I missing something here?
Thanks in advance for helping me.