noncoding RNAs

[victoryhe]

Hi,

how can i get how many transcripts map to rRNA genes, tRNA, snoRNA, microRNA, lincs ,etc, respectively? manually do i count them? is there any tool or package to do it?

any tips would be appreciated,

[NicoBxl]

align your reads against the rfam and mirbase databases

[heytreeful]

if you're dealing with small RNA seq, mirTools and DSAP are two online pipelines that automatically do the alignment for you (mirTools is better I think). You can see if it accepts longer reads.

[victoryhe]

not small RNA, i am taking a look at RNA-Seq data. for this, rFAM is better, right? anything else?