How should I count the percentage of messenger RNA and ribosomal RNA in the samples

Question

[FAST_GENOME]

Dear All

We have some E coli. total RNA-seq data and my PI would like to count the percentage of messenger RNA and ribosomal RNA in the data. My idea is mapping the data to the transcriptome and rRNA data separately and then count the reads#.

Do you think this is a doable plan? But, I have no idea where to find the transcriptome and rRNA reference for the E coli.

Is there is an alternate way to do this analysis? Any suggestion will be appreciated.

Thanks.

AL

[GenoMax]

Hello archie.w.lee!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=80182

This is typically not recommended as it runs the risk of annoying people in both communities.

[FAST_GENOME]

Got it, thanks for the remind.

Answer 1

[jinxinhao1988]

When I do the C.reinhardtii transcriptome analysis, I found all the rRNA of it and made a rRNA reference. Then I used the RNA-Seq data to map with the rRNA reference. and then calculate the ratio of rRNA. As for how to make the reference, you can search in the NCBI. in the E.coli genome page, search the rRNA and gathered all the reads. Since E.coli genome is very small. I guess it's not a complex process.

[FAST_GENOME]

Thank you, I will try.