SchulzLab/Aeron

Remaining adapter sequences

cnk113 opened this issue · 3 comments

cnk113 commented

Hello,

I was wondering if the inputs can handle adapter sequences between the fused transcripts without too much problems?

Thanks,
Chang

SchulzLab commented

Dear Chang,
I don't understand how there could be adapter sequences between the fused transcripts. The adapters are added to the transcripts that are being sequenced, and the hypothesis of fusion transcripts is, that these transcript exist in the cell due to biological mechanisms, such as translocation in a cancer cell.

Therefore, I don't think that your case can happen. Or do you have some other datasource in mind?

Hope that helps,
Marcel

cnk113 commented

Ah well I'm looking to see if it can detect chimeric PCR transcripts and to see if it can map both (or more) transcripts with an adapter sequence in between.

SchulzLab commented

I see. Well AERON allows for a large number of sequencing errors so if there was a short adapter at either end of the chimeric read, it may be able to find the alignment of the remaining read pieces to the genes.
You could simulate the case you have in mind and see whether AERON finds it. We have not tested it for this task.