Closed SergioRodLla closed 1 year ago
I would like to ask you about which is the current criteria for considering a locus to be a MIRNA according to the pipeline. Does this only apply to plant microRNA annotation as you discussed in your paper? I'm using mouse small RNA data.
Why can the "Length" of the locus in the Results.txt file be bigger than ~24 nt and still be considered as a MIRNA? How does the length relate to the number of reads of each length reported for every locus? (I'm probably getting this idea wrong).
Finally, would you recommend to use this tool for identifying other types of sRNA such as tsRNA, siRNA, mRNA, ...? My goal is to identify the proportion of each type that I have in my samples
and I wonder if ShortStack can be suitable if I provide other databases in the --knownRNAs parameter.
--knownRNAs
option has been renamed to --known_miRNAs
to make its function more clear. This parameter is only meant to enhance MIRNA locus finding by using the alignment positions of user-determined mature miRNAs to nucleate searches for loci that meet MIRNA accumulation and secondary structure criteria. It is not suitable for other types of sRNA annotations. You can always just align other RNAs you have to your genome and use bedtools intersect to correlate your alignments with ShortStack's sRNA loci.Thank you for the clarifications!
Hello,
First of all thank you for developing ShortStack pipeline, I'm new to these world of analyzing small RNA-seq data and I found your tool very useful for the identification/annotation step. I would like to ask you about which is the current criteria for considering a locus to be a MIRNA according to the pipeline. Does this only apply to plant microRNA annotation as you discussed in your paper? I'm using mouse small RNA data. Why can the "Length" of the locus in the Results.txt file be bigger than ~24 nt and still be considered as a MIRNA? How does the length relate to the number of reads of each length reported for every locus? (I'm probably getting this idea wrong). Finally, would you recommend to use this tool for identifying other types of sRNA such as tsRNA, siRNA, mRNA, ...? My goal is to identify the proportion of each type that I have in my samples, and I wonder if ShortStack can be suitable if I provide other databases in the --knownRNAs parameter.
Thanks a lot in advance! Sergio