Question: FastQC report analysis
0
gravatar for anjuraas
7 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 • 472 views
ADD COMMENTlink modified 5 months ago by Charles Warden6.9k • written 7 months ago by anjuraas10

That seems short, what kind of data is this?

ADD REPLYlink written 7 months ago by jrj.healey12k

this is miRNA dataset downloaded from SRA

ADD REPLYlink written 7 months ago by anjuraas10
1

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

ADD REPLYlink written 7 months ago by h.mon26k

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

ADD REPLYlink written 7 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 7 months ago by h.mon26k

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

ADD REPLYlink written 7 months ago by anjuraas10
1
gravatar for Charles Warden
5 months ago by
Charles Warden6.9k
Duarte, CA
Charles Warden6.9k 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 5 months ago by Charles Warden6.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1839 users visited in the last hour