[Swiftng-users] Image offsets

[Bernd J. <ber...@pa...>]

Nava,

 

More questions regarding the xml output.

 

 

> > Image offsets:

> > 

> > ==============

> > 

> > I think there are few issues with the runreport files:

> > 

> > The XML tags are somewhat obvious:

> > 

> > Base = A=0,C=1,G=2,T=3

> > 

> > Cycle = cycles of solexa run = length of sequence (Problem the cycle

> > numbers: for me they go from 0-9, 0-10, 0-10, 0-6) = 39 cycles, but we
only

> > use 36!!!)

> 

> ah ok. I think this is an issue with load_cycle. The pipeline loads

> reads in batches of 10 by default. During each back it also pulls in the

> reference cycle images, that's putting the numbering out. I'll fix this

> but as a temporary workaround you should be able to change load_cycle to

> 37 and the offsets should be correct.

 

>From looking at the offsets I have to believe that the last image is the
reference image for the offsetmaps blocks following the first. 

I.e. There are four blocks of "offsetmaps". In the first block the first
entry for each base is the reference (base =0,1,2,3 cycle=0). In the
following three blocks (for a 36 cycle run) the last "offsetmap" block
refers to the reference image (base =0,1,2,3 cycle=10,10,6).

Now I would expect the offset of the reference image to be zero (0), but it
seems not the case for the last three "offsetmaps" blocks. Could you please
elaborate on this?

 

Also, when are you planning to release a new version of the swift program
with an updated xml output?

Do you plan to provide a converter tool to change old xml output to new?

As I am currently developing the image/cluster retrieval I would be
interested in those tools because I don't want to redo everything in a week
or two ;)

I am trying to do this in R. Do you by any chance have already some tools
related to this?

 

Yet another note: Do you know how to do the same thing with the Illumina
image analysis. I.e. how can I get the actual raw data from the images for
each cluster (image intensities)?

 

Thanks so much for your kind help,

 

Bernd