FastQC report analysis

Question

[anjuraas]

my FastQC report shows sequence length as 20-36.Can I accept the sequence?

Basic Statistics                       -pass
Per base sequence quality     -pass
Per tile sequence quality        -pass
Per sequence quality scores  -pass
Per base sequence content    -fail
Per sequence GC content      -fail
Per base N content                 -pass
Sequence Length Distribution -warning
Sequence Duplication Levels  -fail
Overrepresented sequences  -fail
Adapter Content                      -pass

[Joe]

That seems short, what kind of data is this?

[anjuraas]

this is miRNA dataset downloaded from SRA

[h.mon]

Then it should be fine, and my guess is adapters have already been removed.

[anjuraas]

In FASTQC report, adapter content is pass.that means adapters has been removed,right?

[h.mon]

If this is miRNA, then it is fine. If this is mRNA / whole genome / etc, then it is too short. How long the sequence length should be? Was this a single end, 50bp run?

[anjuraas]

This is miRNA dataset from SRA.it is single end run of 57.0 Mbp.

Answer 1

[Charles Warden]

I think it is better to visually review the FastQC results to make your assessment. For example, if you look at enough categories, I think you will encounter some with "warning" or "fail" status, but you may still be able to get useful results from the data.

FastQC has some known sequences that it searches for (and uses those to annotate over-representative sequences). So, I would recommend looking at the individual top over-representative sequences (to check their annotation and/or BLAST them to make sure they are from your organism of interest).