Fastqc shows over-represented sequence with no sequence given?
2
3
Entering edit mode
9.4 years ago
chapmansm13 ▴ 50

Hi,

I uploaded a sequence file to FastQC and it showed an over-represented sequence so I trimmed it with cut-adapt. I re-ran the trimmed file through fastQC and it shows another over-represented sequence with a different count and percentage saying 'no hit' and not showing the bases of the sequence?

Does anyone know why its not showing the bases of the new hit??

Thanks

sequencing • 7.4k views
ADD COMMENT
0
Entering edit mode
9.4 years ago
John 13k

If im not mistaken, the 'No Hit' refers to possible sources for the over represented sequence (i.e., known primer/adapter sequences)
So this simply means that whatever your over represented sequence is, FastQC doesn't know about it in its contaminants list.

This isn't really a problem - just cut-adapt on whatever you think the sequence is. Better yet, paste the sequence into Google to find out what it is :)

In future, you will get a better answer if you screenshot your data/problem :)

ADD COMMENT
1
Entering edit mode

Hi, its not actually telling me what the sequence bases are.

ADD REPLY
0
Entering edit mode

What the... o_o
...well, er, i'd like to say don't worry about it because 5547 of anything is not a lot.
... but since FastQC is clearly not behaving itself, perhaps you should run a different over-represented sequence tool on it.

ADD REPLY
0
Entering edit mode

Ok thanks, Are there any tools you would suggest?

ADD REPLY
0
Entering edit mode

Sorry I don't know of any other than FastQC, but I'm sure a quick Google will bring something up.

I wrote a module for SeQC that does this, but its a bit technical (you'd need to know Cypher or have Gelphi installed..?) and its very unpolished. If you're willing to wait a month I can help, hahah, but your best bet is to just find another tool like FastQC :)

ADD REPLY
0
Entering edit mode
3.6 years ago
MboiTui ▴ 20

This is the result of not removing sequences with 0 length after trimming (hence why it is not reporting the base pairs). Set the minimum sequence length to more than 0 and it will solve the issue

ADD COMMENT

Login before adding your answer.

Traffic: 1799 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