classification of small RNA-seq

Question

[Sam]

How to categorize smallRNA reads according to different subtype such as miRNA,snoRNA,rRNA, tRNA, snRNA ?

Also same question is here Mapping microRNA reads to Genome and non-coding RNAs

Thanks

[WouterDeCoster]

Please elaborate. If a question fits in one sentence you usually didn't explain it well enough.

[Buffo]

Look at this microRNA Sequencing Data Analysis Guideline

Answer 1

[aka001]

Although your question seems lacking some depth and clarity, I would just point out one way (there are many ways, e.g. prediction, etc.): take the gene biotype information of your's organism Ensembl gtf file (i.e. count your reads using this file). There you can see different biotypes, including what you mentioned (although it's kind of weird if you want to get lncRNA from small-RNA reads).

[Sam]

Hi I have exactly same question as same this link Mapping microRNA reads to Genome and non-coding RNAs Thanks

[aka001]

Currently you are at which step (another way to put it: how did you process your reads)?

[Sam]

I performed adaptor removal and aligned filtered reads against to human miRNAs in miRBase using sRNAWorkbench

[lessismore]

.....the remaining unique sequences were mapped to the radish reference genome which consisted of radish GSS, EST and transcriptome sequences, to analyze the expression and distribution of sRNAs on genome using SOAP2 program [25,26]. Perfectly matched sequences were retained for following analysis. By querying against the NCBI Genbank (http://www.ncbi.nlm.nih.gov/genbank/) and Rfam (10.1) (http://www.sanger.ac.uk/resources/databases/rfam.html) databases, the sRNA sequences matching rRNA, tRNA, snRNA, snoRNA as well as sequences containing poly (A) tails were excluded. The remaining unique sequences were aligned against miRBase 20.0 (http://www.mirbase.org/index.shtml) to identify radish known miRNAs.....

I think you want to do something like this, correct? https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1416-5

[Sam]

yes exactly, are you agree with local NCBI blast against Rfam database and then grep according to each subtype?

[lessismore]

I guess so, check this >> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3554743/pdf/pone.0054111.pdf