Truseq Multiplexing / Minimal number of Samples

[andibody]

Hi,

we have been working for a while with custom barcoded adapters. Successful basecalling seems to depend mostly on sufficient base complexity and we therefore run a minimum of 4 samples per lane.
However, we are testing at the moment illuminas Truseq barcoded adapters and were wondering if they are also prone to camplexity restrictions. Has anybody tested running only 2 or 3 barcodes in a lane? In theory, all basecalling parameters were calculated in read 1 so the reduced complexity shouldn't be such an issue. Any thoughts?

best
A

[ETHANol]

See this thread:

http://seqanswers.com/forums/showthread.php?t=13093

I'll know shortly (I hope) how it goes.

[andibody]

Thanks a lot for the link!
So, are you going to try the low-level pooling experiments?
Interesting protocol, just had a quick look but I'm looking forward to hear how it worked.
From time to time a ChIP-seq sample wouldn't work showing PCR artifacts (stacks of reads at the same position). I think we lost material but we never found out where exactly. If the sample isn't where it should be on the gel during extraction due to the Y-linkers it might explain this loss.

Thanks again & Good Luck