Here is the text of your two posts:

I have Illumina data of 1 x50bp from small RNA library. I am interested in identifying known and novel miRNAs in my plant, whose reference genome is not available. Here first I want to count the reads aligning to non-coding rRNAs like tRNA, rRNA, snoRNA, snRNA, siRNA etc except miRNAs. After removing those reads, I would like to align remaining reads with miRBase using blastn or bowtie to identify known miRNAs. Now problem is that, I want to use Rfam for detecting reads of different RNA class, thus I concatenated the fasta files of 2686 families (2,487,655 sequences) but Rfam v13 sequences does not have proper information of the class they represent in their header. So my concern is how can I count and extract the reads mapping to different classes of RNAs using Rfam.

and

I have Illumina data of 1 x50bp from small RNA library. I am interested in identifying known and novel miRNAs in my plant, whose reference genome is not available. However, first I want to count the reads aligning Exon sense, Exon antisense, Intron sense, Intron antisense. Basically, I want to replicate the information shown in table below. I have gone through the complete publication and they have mentioned the use of Rfam database in "Experimental procedures" section for identifying mRNA. So my question is how can I classify reads as Exon sense, Exon antisense, Intron sense, Intron antisense using Rfam or any other databases?

It looks like you are referring to the same experimental dataset in both posts. You have added the request of how can I classify reads as Exon sense, Exon antisense, Intron sense, Intron antisense.

You can always edit the first post and add this a second requirement. This will automatically bring your post back up to main page. It is my understanding that if you did a smallRNA prep then it is not going to work for normal mRNA discovery.

We make an effort to keep threads focused on topics (with answers in one place) so the information is easy to find for others who search for it in future. That is the only reason this post has been closed with reference to your previous one.