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 <[email protected]>
Date: October 9, 2009 10:08:25 AM CDT
To: "[email protected]" <[email protected]>
Subject: RE: SFC#00118080 - Control over file name format?
Reply-To: [email protected]
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 [email protected] 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: [email protected]
Web: www.illumina.com
-----<Email Received>-----
From: [email protected]
Sent: 10/08/2009 07:47 AM PDT
To: [email protected]
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
[email protected]
(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
[email protected]
(256) 327-0473 (p)
(256) 327-0966 (f)
Room 4005
601 Genome Way
Huntsville, Alabama 35806
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