Question: How should I count the percentage of messenger RNA and ribosomal RNA in the samples
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gravatar for archie.w.lee
5 months ago by
archie.w.lee40
archie.w.lee40 wrote:

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

rna-seq • 226 views
ADD COMMENTlink modified 5 months ago by jinxinhao198850 • written 5 months ago by archie.w.lee40

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.

ADD REPLYlink written 5 months ago by genomax49k

Got it, thanks for the remind.

ADD REPLYlink written 5 months ago by archie.w.lee40
1
gravatar for jinxinhao1988
5 months ago by
China/Beijing
jinxinhao198850 wrote:

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.

ADD COMMENTlink written 5 months ago by jinxinhao198850

Thank you, I will try.

ADD REPLYlink written 5 months ago by archie.w.lee40
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