Hi All 
,
I'm new to RNAseq and have just recieved my libraries from the sequencer. I've used the Illumina kit to prep and set the Solexa for 75bp reads. Tophat was used to allign my reads to the reference genome. The data look, for the most part, pretty good. I'm finding new transcripts, my tags map very well to the reference genome but, I'm finding a high number of tags that map to the 3' UTRs of many genes. They really seem to be overrepresented. The only thing I can think of is that perhaps there was incomplete reverse transcription in my cDNA synthesis?
So far I've only looked at one library so it's possible this is just an artefact but I'm lost for an explanation. Any help would be appreciated.
,I'm new to RNAseq and have just recieved my libraries from the sequencer. I've used the Illumina kit to prep and set the Solexa for 75bp reads. Tophat was used to allign my reads to the reference genome. The data look, for the most part, pretty good. I'm finding new transcripts, my tags map very well to the reference genome but, I'm finding a high number of tags that map to the 3' UTRs of many genes. They really seem to be overrepresented. The only thing I can think of is that perhaps there was incomplete reverse transcription in my cDNA synthesis?
So far I've only looked at one library so it's possible this is just an artefact but I'm lost for an explanation. Any help would be appreciated.
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