For micro RNA (miRNA) data, the following aligners are recommended specifically for these short sequences:
Does anyone know how the Rsubread align function compares to these? Has anyone performed any comparisons? I use Rsubread for RNAseq and it would be convenient to use it also for miRNAseq, but I am a little concerned and wonder whether I need to invest time in conducting some comparisons.
I have just noticed one potential problem with Rsubread align function when applied to miRNAseq: When I use the annotation file from mirBase (hsa.gff3) instead of the built-in annotation or the ensembl GTF file, then the Gene IDs in the counts (rownames) and annotation output from Rsubread-align are all NA (see code below).
counts_TH14_uniqtrue_annotMirBmature.out <- featureCounts(files=mapped.flist,
# use mirBase GTF file and feature = miRNA (mature miRNA)
GTF.featureType="miRNA", GTF.attrType="miRNA", useMetaFeatures=FALSE, ...
Many thanks, Ina
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
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attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
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