Illumina GAII sequencing errors

[jobu]

Dear All,

I've got deep-sequencing data for bioinformatic processing, that show some remarkable errors, I can't explain to myself.

What I am observing is small in absolute numbers:
a 1000 out of a million short-reads contain 'N's, so this would be a tiny fraction of sequences.

As I understand the error-rate increases towards the end of sequences and while I can see this in my data too this is not bothering me.

However, I'm stumbling about the fact, that 80% of those misreads specifically carry an 'N' at Position 13.
Does anybody has a hint that could help to explain this?

kind regards
Jochen

[GenoMax]

Jochen: There could be several possible causes (e.g. fluidics, bubble in the lane).

You may want to talk with the facility that generated the data to see if this run had similar problems with other sample lanes. Generally a good service provider should re-run such samples for free if the problem lies on their end.

[jobu]

Illumina GAII sequencing errors

GenoMax,

many thanks for your reply.

I'll try to find out more about this.
Though I do not have a direct contact to the people that originally ran that deep-sequencing yet, I guess the contact can be made.

I have to add:
The data affected by what I described consists of 8 different data-sets, derived from 8 different lanes and each & every set is showing those 'N's at Pos. 13.


kind regards
Jochen

[GenoMax]

I have to add:
The data affected by what I described consists of 8 different data-sets, derived from 8 different lanes and each & every set is showing those 'N's at Pos. 13.

kind regards
Jochen

If those 8 lanes came from the same flowcell then that almost certainly indicates some kind of an issue with that specific run. You should definitely contact the folks who did the sequencing if that is true.