Question: classification of small RNA-seq
0
gravatar for Sam
14 months ago by
Sam80
Sam80 wrote:

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

rna-seq alignment • 648 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by Sam80

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

ADD REPLYlink written 14 months ago by WouterDeCoster35k

Look at this microRNA Sequencing Data Analysis Guideline

ADD REPLYlink written 14 months ago by Buffo1.2k
1
gravatar for aka001
14 months ago by
aka001180
Sweden
aka001180 wrote:

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).

ADD COMMENTlink written 14 months ago by aka001180

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

ADD REPLYlink modified 14 months ago • written 14 months ago by Sam80

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

ADD REPLYlink modified 14 months ago • written 14 months ago by aka001180

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

ADD REPLYlink written 14 months ago by Sam80

.....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

ADD REPLYlink modified 14 months ago • written 14 months ago by lessismore550

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

ADD REPLYlink written 14 months ago by Sam80
1

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

ADD REPLYlink written 14 months ago by lessismore550
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