Entering edit mode
5 weeks ago
deniselavezzari
•
0
Hi,
I have sequencing data from extracellular vescicle done with Qiaseq miRNA library kit with UMI. I've align the data to the human genome with bowtie2 and removed duplicates with umitools. Now, I'm trying to identify the miRNA in the data using subreads featureCounts/mirdeep2 and I'm trying also with bedcov. I have different results, bedcov used as it is gives me the highest number of miRNA covered. Do you think it could be a good solution to identify known miRNA?
Hard to tell without knowing the actual differences between the tools and seeing the outputs, but my 2 cents are that you get leads from subread (I guess featureCounts?) since it doesn't consider multimappers. Also just a recommendation, since you are not looking for novel microRNAs and the human is quite extensively studied, I would recommend aligning to miRBase directly