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

[Martin Morgan]

Hi Michael -- I'll respond off-list; this level of detail is really
internal to the package. Martin

Michael Muratet wrote:
> 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
> 
> 
> 
> 
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793