Gene Expression Tag Table Software Now Available

arielpaulson · 08-18-2008, 04:56 PM

I've had several of requests to make our tag table creation software publicly available, so now it is.

http://research.stowers-institute.or...ay/tag_tables/

This is designed for use with Illumina's GEX protocol. There are two halves. The first script uses an Ensembl database to produce tag tables which are similar to Illumina's proof-of-concept tables for human and mouse. However it does not follow their classification rubric, we developed our own. The second script consolidates and annotates the aligned data; right now only Eland alignments are supported, specifically the s_*_eland_result.txt format.

It's written in pretty transparent perl, and it haven't bothered with use strict or -w or anything (yet). You're welcome to hack around with it. If people like it, I'll develop it further. There are already some developments planned, which are listed on the site. The site also goes into detail regarding the internal operations of the software and assumptions about genomic features. There's more to post there so I'll be working on it over the next couple of months.

Thank you again Kevin Carr for helping me test/improve this software!

Please direct any feedback to apa[at]stowers-institute[dot]org.

Ariel Paulson
Programmer Analyst
Microarray Group
Stowers Institute for Medical Research

******Admin Edit Below******
Stickied in the Bioinformatics forum, originally from this thread: http://seqanswers.com/forums/showthread.php?t=284

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08-18-2008, 04:56 PM	#1
arielpaulson Member Location: Kansas City Join Date: May 2008 Posts: 14	Gene Expression Tag Table Software Now Available I've had several of requests to make our tag table creation software publicly available, so now it is. http://research.stowers-institute.or...ay/tag_tables/ This is designed for use with Illumina's GEX protocol. There are two halves. The first script uses an Ensembl database to produce tag tables which are similar to Illumina's proof-of-concept tables for human and mouse. However it does not follow their classification rubric, we developed our own. The second script consolidates and annotates the aligned data; right now only Eland alignments are supported, specifically the s__eland_result.txt format. It's written in pretty transparent perl, and it haven't bothered with use strict or -w or anything (yet). You're welcome to hack around with it. If people like it, I'll develop it further. There are already some developments planned, which are listed on the site. The site also goes into detail regarding the internal operations of the software and assumptions about genomic features. There's more to post there so I'll be working on it over the next couple of months. Thank you again Kevin Carr for helping me test/improve this software! Please direct any feedback to apa[at]stowers-institute[dot]org. Ariel Paulson Programmer Analyst Microarray Group Stowers Institute for Medical Research ***Admin Edit Below**** Stickied in the Bioinformatics forum, originally from this thread: http://seqanswers.com/forums/showthread.php?t=284