Hi,
Is there any generally accepted best way to align and measure the expression of micro-RNAs ? Looking at the literature it seems that pretty much every group has its own custom way of doing the alignment and assessing the number of reads for each microRNA. Some of the more generic aligners to be used seemed to be Bowtie, Shrimp, or Novoalign, but what about alignment parameters ? With more strict alignment parameters it is hard to detect isoMirs and with more liberal ones it is not clear if the mapping is correct. Some groups align against hairpins, others against mature microRNA sequences.
The ideal pipeline would probably take the input sequences, cut adapters and generate read counts for each mature microRNA/isoMir.
Any suggestions for how to build and parametrize such a pipeline ?
Thanks a lot !
Is there any generally accepted best way to align and measure the expression of micro-RNAs ? Looking at the literature it seems that pretty much every group has its own custom way of doing the alignment and assessing the number of reads for each microRNA. Some of the more generic aligners to be used seemed to be Bowtie, Shrimp, or Novoalign, but what about alignment parameters ? With more strict alignment parameters it is hard to detect isoMirs and with more liberal ones it is not clear if the mapping is correct. Some groups align against hairpins, others against mature microRNA sequences.
The ideal pipeline would probably take the input sequences, cut adapters and generate read counts for each mature microRNA/isoMir.
Any suggestions for how to build and parametrize such a pipeline ?
Thanks a lot !