[pmiguel]

I should add that Illumina deserves a lot of credit for how they handle storing data off-site. We have a gigabit line to our storage server and just mapped that server as a samba share. But, in testing, cutting off the samba connection in the midst of the run did not even generate an error. The instrument appeared to seamlessly fail over to saving the data locally. Then, when the connection was restored the data was gradually transferred.

I do not know that the Dell console computer even has enough storage locally to save the raw .TIFFs. I think it has a RAID of four 2 TB drives. So, to a first approximation, that would mean that saving the image data for a run is simply impossible without an off-site storage solution.

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Phillip
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Phillip

[rallapag]

Manual configuration of "Configurable Template Generation Cycles option" in the SCS2.9/RTA1.9; any update on this?? anyone tried it??

I do understand Felix Krueger's explanation on this (comparison to "bareback")

After talking to our Illumina rep we don't have any reason to believe that the "Configurable Template Generation Cycles" option is any different from the previous unofficial option "--image-flags". Thus, I would imagine that the basecalls would still suffer from mysteriously bad qualities, see the Supplementary Figures linked in the first post of this thread.

can the following post from Simon Andrews, explains the reason for predominance of bad qualities from Illumina pipeline

...........one of the illumina filters looks for deteriorating quality and then flags all remaining bases with low quality scores, even if the quality later improves (the so called 'killer Bs'. You can turn this off using the undocumented parameter NO-EAMSS when processing which will preserve the original qualities. If you then trim your sequences to just your bases of interest then the qualities there should be OK.

[amitra]

Hi Guys!
I am very interested in this problem, since we have been unsuccessful in sequencing a sample with a custom barcode 'TCGAGGTAGTA' attached, probably due to lack of diversity.

I may get a one time opportunity to visit and potentially work with our sequencing facility for re-sequencing of our sample.
We would have an opportunity to change some default options on RTA software.

Can the experts please guide us as to the best way to go with a HiSeq 2000 sequencer with a single flow cell 50bp run?

I will carry with me 5x3TB hard drive to the facility and if needed configure it as a RAID0 or RAID5 on the RTA machine to store TIFF files.