Hi Chirag,
We know that there are polyAs in unmatured snoRNAs in patient becoz we have analysed the abundance of only polyA and total snoRNAs. The abundance of polyA snoRNAs were quite high in Patient vs Normal (qPCR data). This suggests that the proportion of unmatured snoRNAs are high in patient. So we did sequencing to identify the sequence and length of the polyAs in particular snoRNAs.
Here's the picture showing the maturation of H/ACA box snoRNAs.
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sethugunja •
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sethugunja •
Hopefully others will reply with a premade tool, but I would think the general idea would be to first perform mapping as normal and then take the unmapped reads and split them to allow anchoring. You'd then try to map the anchors. The 3' extension would be the sequence of the remainder of an anchored read that maps on the 3' end. This is sort of how tophat works, though it'd make more sense to simply write a custom pipeline than to modify tophat.
Thank you for your prompt reply,
Can you please explain how to split and anchor them?
Sethu
Whatever program you write/find would take each read and segment it into non-overlapping stretches (of maybe 15-20 bases each). In this context, anchoring would be performed by simply mapping these segments to either the genome or a library of small RNAs (this is probably more efficient).