Question: Small RNA library contaminated by primers?
gravatar for eva.lucarelli
5 weeks ago by
eva.lucarelli0 wrote:


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.


ADD COMMENTlink written 5 weeks ago by eva.lucarelli0

Small RNA data requires special handling. Find out what kit was used for the data. Then follow up with specific instructions for that kit/method.

ADD REPLYlink written 5 weeks ago by genomax92k
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