I have just tested miRanalyzer and am now realizing that it may not use a very recent version of miRbase. The database construction is not trivial for this program however, and the bowtie indexes for the mature and hairpin screens are provided with the miRbase program. I am guessing that this is because the miRbase sequences are modified to align with bowtie.
I have tried making my own indexes and running bowtie with the miRbase fasta files, without success.
Does anyone have any experience with a good program to analyze miRNA, that reports known mature and hairpin structures from miRbase and can be updates regularly for use in a pipeline?
thanks,
holly
I have tried making my own indexes and running bowtie with the miRbase fasta files, without success.
Does anyone have any experience with a good program to analyze miRNA, that reports known mature and hairpin structures from miRbase and can be updates regularly for use in a pipeline?
thanks,
holly
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