Hello, 

I am still trying to map probes on the Nimblegen Zebrafish 12 x135K Expression to the Zv9 version of the zebrafish genome available from Ensembl!  I am very reluctantly pursuing an alignment approach to annotation as the original annotation provided with the array is quite outdated.

I performed a gapped alignment using the individual probe sequences (60-mers) from the array using TopHat and loaded the results into Bioconductor as a GappedAlignments object.  I have made a TranscriptDb object using the Zv9 genome from Ensembl.  Next, I plan to use findOverlaps for the annotation. What is the best way to get the overlaps (by exon, cds, or by transcript)?  I am a little concerned that using transcriptsByOverlaps might be a bit too broad and result in mapping reads to multiple genes (for example transcripts in the genome that have overlapping genomic coordinates). By contrast, mapping with exonsByOverlaps and cdsByOverlaps might be too restrictive and miss information in the UTR's.  My gut feeling is that annotating by cds is the "in-between" approach.  What is the recommended approach for RNA-seq?  As you can tell, I am quite new to this!

Thanks in advance for your help, 
Ravi


	[[alternative HTML version deleted]]

