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Old 02-16-2011, 07:25 AM   #1
rkarra
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Location: NC

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Default Annotation of Nimblegen Zebrafish Array

Hi,

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 The probes were derived from a variety of sources, many of which are now out of date.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?

Thanks!
Ravi
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Old 02-16-2011, 08:39 AM   #2
ffinkernagel
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Default

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.
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