Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
GS Jr and Nimblegen yaximik 454 Pyrosequencing 0 12-12-2011 06:12 AM
BWA aligner - zebrafish miRNA naluru SOLiD 0 12-09-2010 01:08 PM
Nimblegen Probes aleferna Bioinformatics 1 08-10-2010 01:25 PM
PubMed: Parallel DNA pyrosequencing unveils new zebrafish microRNAs. Newsbot! Literature Watch 0 04-29-2009 06:00 AM
Nimblegen linkers suludana Illumina/Solexa 6 11-13-2008 02:47 PM

Thread Tools
Old 02-16-2011, 07:25 AM   #1
Junior Member
Location: NC

Join Date: Feb 2011
Posts: 1
Default Annotation of Nimblegen Zebrafish Array


I am currently working with some gene expression data using the Nimblegen Zebrafish 12 x135K Expression platform. Unfortunately, my analysis has been limited by annotation. The probes were derived from a variety of sources, many of which are now out of date.

A bit reluctantly, I would like to remap the array to transcripts from the latest zebrafish genome available (Zv9) at Ensembl so that I can then use biomaRt (via Bioconductor) for subsequent annotation. I would like to use TopHat to align the probe sequences on the array to Zv9. Is this reasonable? Are there any issues with "strandedness" for this kind of approach?

rkarra is offline   Reply With Quote
Old 02-16-2011, 08:39 AM   #2
Senior Member
Location: Marburg, Germany

Join Date: Oct 2009
Posts: 110

I've in the past used Bowtie both on a cDNA index and a genomic index created from an Ensembl genome for Agilent arrays. Works well, though of course the 'mismatch match to N transcripts of 1 gene beats a perfect match 5kb downstream of a gene on the genome'... decision tree is a bit tedious.
ffinkernagel is offline   Reply With Quote

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 11:00 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO