RNAseq RNA content

Question

[doramora]

How can I check my row RNA from RNAseq?

I want to test my RNA and get the percentage of mRNA and each type of rRNA. How can I do this in Linux terminal?

[ATpoint]

What is "row RNA"?

Answer 1

[ntsopoul]

I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which method you purified and constructed your library. Did you do polyA enichement? In this case you enriched for mRNA. Did you do rRNA depletion? In this way you have mRNA plus ncRNA and small RNAs in your mixture. I am not aware of any method where you sequence "total RNA". Another way to estimate your rRNA content would be to run tapestation.

Answer 2

[noodle]

There are many tools for this. I recommend gatk (picard) CollectRnaSeqMetrics or alternatively RSeQC

and then run multiqc to create a nice html-report

each type of rRNA. How can I do this in Linux terminal?

depends on reference genome, annotation file (bed, gff, gtf), etc...you can parse out rRNA and mRNA from a bed file and then calculate coverage on those genes using one of many R and/or python packages. DESeq2 is a popular.