Hello all,
I have the task of analysing a smallRNA data set with a focus on microRNAs in tomato. The task (at least sounds) simple: how many known and novel microRNAs are there in our samples and how does this change with a particular treatment? So I'm looking for both qualitative and quantitative data.
The mirdeep-p pipeline requires substantial editing of files so I may have missed something along the way when making the required intermediate files. Attached is a short example from one such sample after completing section 4 of the guide "RETRIEVING EXPRESSION PATTERNS OF KNOWN MIRNA GENES AND OBTAINING THE OPTIMAL LENGTH OF PRECURSORS". Specifically, why do I have '_4' or '_6' after some of the microRNA gene names and what do the associated scores mean? My initial thought was it might have something to do with the mirbase gff file detailing the known microRNAs (?). There is no further advice in the guide and the correspondence emails on the paper for the package are no longer active. Any thoughts are much appreciated.
Deb
Dear Deborah,
I don't know the mirdeep-p pipeline, but I can recommend the miRDeep2 pipeline, both for predicting novel miRNAs and also for quantification (see link below).
Best,
Anja
https://www.mdc-berlin.de/36105849/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/documentation
Hi Anja,
Thanks for the link however I unfortunately can't use mirdeep2 since there are subtle but important differences in classifying microRNAs in plants and an alternate algorithm is required to take these into account. mirdeep itself is definately less complicated to run than mirdeep-p! I do think that the method of quantification of known microRNAs is the same between these two platforms but I didn't get a response from the authors. Any thoughts?
Deb
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