Small RNA library contaminated by primers?
0
0
Entering edit mode
9 months ago

Hello,

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.

Eva

RNA-Seq FastQC primer trimming adapter trimming • 228 views
ADD COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1923 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6