SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
documentation for ABySS harrb Bioinformatics 1 11-23-2010 09:18 AM
Discussion the general pipeline to analyze 454, Illumina/Solexa data edge General 1 09-09-2009 07:29 PM
Paired end solexa (goat/gerald) pipeline bioinfosm Bioinformatics 4 02-02-2009 12:39 PM
Solexa pipeline cgjkjk Bioinformatics 0 01-23-2009 08:47 AM
New version of Solexa GA pipeline tool bioinfosm Bioinformatics 2 05-28-2008 08:51 AM

Reply
 
Thread Tools
Old 10-02-2008, 02:45 AM   #1
jwaage
Member
 
Location: Copenhagen, DK

Join Date: Sep 2008
Posts: 16
Default Solexa Pipeline documentation, or similar?

Hello everyone,

I've been given the privilege to get to crunch trough our lab's first round of Solexa reads of small RNAs. I've worked on some earlier data, and plan on using MAQ for mapping, and perhaps CLCbios Genome Workbench, as soon as we get a license (expensive!!) - now, I need a little more information on the general Solexa Pipeline (quality scores, file formats (fastq vs. raw?), and so on) - are these documents in any way accessible publicly?

Btw, thx for the great information I've found so far on this forum!

Regards,
JW,
Uni. of Copenhagen, Denmark
jwaage is offline   Reply With Quote
Old 10-02-2008, 02:19 PM   #2
new300
Member
 
Location: northern hemisphere

Join Date: Mar 2008
Posts: 50
Default

Quote:
Originally Posted by jwaage View Post
I've been given the privilege to get to crunch trough our lab's first round of Solexa reads of small RNAs. I've worked on some earlier data, and plan on using MAQ for mapping, and perhaps CLCbios Genome Workbench, as soon as we get a license (expensive!!) - now, I need a little more information on the general Solexa Pipeline (quality scores, file formats (fastq vs. raw?), and so on) - are these documents in any way accessible publicly?
As far as I know the pipeline documentation isn't made available unless you own an instrument. They have been fairly good about giving people who don't have an instrument access to the software, I believe you need to register through iCom: http://icom.illumina.com/.

I have a few little reports which might be of use, this one on how parts of the pipeline work:

http://www.genographia.org/portal/to...eline.pdf/view

and this one on next-gen stuff in general:

http://www.genographia.org/portal/to...rimer.pdf/view

People here are very helpful so I'd ask away.
new300 is offline   Reply With Quote
Old 09-15-2009, 05:43 AM   #3
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

Those genographia links are dead now
maubp is offline   Reply With Quote
Old 09-15-2009, 06:56 AM   #4
new300
Member
 
Location: northern hemisphere

Join Date: Mar 2008
Posts: 50
Default

They are now online here:

http://sgenomics.org/mediawiki/index.php/Genomics
new300 is offline   Reply With Quote
Old 09-15-2009, 07:04 AM   #5
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

Cool

I'm a puzzled about your PHRED/Solexa mapping table though. Isn't -5 taken as the lowest Solexa FASTQ score, thus while the log mapping does mean PHRED 1 would map to Solexa -5.87 (2dp), in practice it should be mapped to -5.0 (thus ASCII 59 ";" not ASCII 58 ":").

Thanks
maubp is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:43 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO