Hi,

For micro RNA (miRNA) data, the following aligners are recommended specifically for these short sequences:
    MicroRazerS www.seqan.de/projects/microrazers/
    mrFAST mrfast.sourceforge.net/
    mrsFAST mrsfast.sourceforge.net/Home
    PatMaN bioinf.eva.mpg.de/patman/
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,
     annot.inbuilt="hg38", chrAliases=NULL,
    # use mirBase GTF file and feature = miRNA (mature miRNA)
    annot.ext="/home/inah/Rsubread_miRNA/RefGTF/hsa.gff3",
    isGTFAnnotationFile=TRUE,
    GTF.featureType="miRNA", GTF.attrType="miRNA", useMetaFeatures=FALSE, ...

Many thanks, Ina

sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=en_US.UTF-8    
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Rsubread_1.22.3

loaded via a namespace (and not attached):
[1] tools_3.3.1

As I replied to the email you sent me regarding your featureCounts question, the 'GTF.attrType' parameter in your command should have a value 'ID'.