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Old 04-23-2013, 11:45 AM   #1
illuminaGA
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Location: Atlanta

Join Date: Dec 2012
Posts: 70
Unhappy Lots of "N" in the barcode.

Dear All

I am new to NGS and GAII.

After several test running ,we have a big problem.

We usually have 6 samples with different barcode(index 2,3,4,7,9,10) in one lane. We have 3.5G data totally in each lane, but the CASAVA only can demultiplexing 64M.

Most of data under Undetermined_indices fold are like this.


@=78@==<:=BDDDDGEGG?===B@>ACBAGGGG@DD==>EEE?EDGE3GEEC>>,838<E>>C???D?=6(/9?:?########################
@ILLUMINA-8ACF53:7:FC:1:52:5835:9761 1:N:0:NNNNGN
TAAACTTTATAATTAAAAAAAAATGCTCATTTGAGCTGCAATAGTTTTACTAACTTTTAATGTCTTAATTCAAATACCCAGTTTCCATAACATAATATCTA

There lots of N in the barcode,so CASAVA cann't demultiplex samples.

We have a little bit overclustering. %PF of my sample is only 29.5+/- 27.32. Is this the main reason?

How to make troubleshooting with this?

Thank you so much.
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