[Bioc-sig-seq] Fwd: SFC#00118080 - Control over file name format?

[Michael Muratet]

Greetings

The latest version of the Illumina SCS software (v2.4) writes  
intensity files to network disk storage in separate folders for each  
cycle and without leading zeros, e.g., s_1_10.cif. The position files,  
however, do have leading zeros, e.g., s_1_0010_pos.txt. I checked the  
manuals and couldn't find a way to change one file name or the other  
and so I checked with Illumina and their response is below.

I think the best way to handle the difference WRT reading *.cif files  
in ShortRead is to make a list of all pos file names, delete the  
leading zeros, and then search that list with the pattern from  
readIntensities. Does that sound reasonable?

Cheers

Mike

Begin forwarded message:

> From: Tiffany Briere <techsupport at illumina.com>
> Date: October 9, 2009 10:08:25 AM CDT
> To: "mmuratet at hudsonalpha.org" <mmuratet at hudsonalpha.org>
> Subject: RE: SFC#00118080 - Control over file name format?
> Reply-To: techsupport-ilmn at illumina.com
>
> Dear Mike,
>
> As I promised, I checked with one of our bioinformaticists.  The  
> naming of intensity files is not controllable through a config  
> setting.
>
> Please contact me through TechSupport at illumina.com if you have any  
> additional questions.
>
> Best regards,
> Tiffany
>
> Tiffany Briere
> Assoc Technical Applications Scientist
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA  92121-1975
> Tel:  800-809-4566
> Fax: 858-202-4766
> E-mail:  TechSupport at illumina.com
> Web:    www.illumina.com
>
>
> -----<Email Received>-----
> From: mmuratet at hudsonalpha.org
> Sent: 10/08/2009 07:47 AM PDT
> To: techsupport-ilmn at illumina.com
> CC:
> Subject: Control over file name format?
>
> Greetings
>
> I have heard that the user has some control over the intensity file
> names (*.cif/*.nse) via a XML config file. It would be great if we
> could get the 'old' style name that has leading zeros rather than, for
> example, s_1_10.cif. I can't find anything in the manuals. Is this
> true? How do you go about it?
>
> Thanks
>
> Mike
>
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmuratet at hudsonalpha.org
> (256) 327-0473 (p)
> (256) 327-0966 (f)
>
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806

Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806