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 The probes were derived from a variety of sources, many of which are now out of date.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 The probes were derived from a variety of sources, many of which are now out of date.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