Question: FastQC report analysis
0
gravatar for anjuraas
23 months ago by
anjuraas10
anjuraas10 wrote:

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
sequence • 1.0k views
ADD COMMENTlink modified 21 months ago by Charles Warden7.9k • written 23 months ago by anjuraas10

That seems short, what kind of data is this?

ADD REPLYlink written 23 months ago by Joe18k

this is miRNA dataset downloaded from SRA

ADD REPLYlink written 23 months ago by anjuraas10
1

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

ADD REPLYlink written 23 months ago by h.mon31k

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

ADD REPLYlink written 23 months ago by anjuraas10

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?

ADD REPLYlink written 23 months ago by h.mon31k

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

ADD REPLYlink written 23 months ago by anjuraas10
1
gravatar for Charles Warden
21 months ago by
Charles Warden7.9k
Duarte, CA
Charles Warden7.9k wrote:

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).

ADD COMMENTlink written 21 months ago by Charles Warden7.9k
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