I use bowtie mapping the smallRNA-seq, but I want to annotate the percent of reads with miRNA, snoRNA, rRNA, tRNA and repeat.
I read the paper is use blast+ and rfam database. Now I don't know which to download in the rfam and how to run the program that make sequence reads classified to major non-coding RNA groups can be viewed as miRNA, snoRNA, rRNA, tRNA and repeat.
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If you have already mapped these reads against the reference genome, you can download genomic coordinates for miRNA, tRNA, rRNA, snoRNA etc using UCSC table browser (http://genome.ucsc.edu/cgi-bin/hgTables?command=start) and can use bedtools or HTseq to count or annotate reads aligned to different small RNAs. Though UCSC annotation for some species of small RNAs won't be as comprehensive as some other resources that are exclusively created for that specie of RNA but it should be able to give you close to the optimal results.
Thanks for reply, My species is pig, so the annotation is not very suffcient. I think blast is more acceptable method.
Hi,
I am planning to do the same requirement as yours. Annotate the percent of reads with miRNA, snoRNA, rRNA, tRNA and repeat for sequenced reads from pig. Would you provide any recommendations?
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