Does anybody trouble for the number of assign beads ?

[Yuki]

Hi all,

I use SOLiD4 , its protocol is Multiplex(barcode) Frangment run.
Usually my sample is ChIP sample.

Though I amplificated 12 libraries and run as usual last time, 4 of 12 libraries were little assign. The number of 4 was ten times or more as little as that of others.
Of course I checked amout of P1-P2fragment by qPCR and collect libraries same range by e-gel.
After I did ePCR using same amout of libraries as a template, I got good results in WFA.

Does anybody know such a trouble?

I have no idea but there is a possibility that the quality of ChIP DNA was bad.
However I cehcked those libraries has P1 and P2 by qPCR and size range was collect.(All libraries were same range.)
Nevertheless, after sequencing the number of assign beads was much different. I couldn't understand.

Other possiblity is the sequence of barcode?? One barcode is easy to assign???

Sorry, but please help me...

[KevinLam]

How are u assigning the reads?
I had the same prob in 3 plus. Due to multiple reasons.

I used wrong library in setup. ( check if majority of reads are in a particular barcode.

Did u allow 1 mismatch?

Check w ur FAS if there's a better hamming sphere file.