Basic steps in prokaryotic RNAseq data analysis

Muhidini · 05-09-2012, 07:27 AM

Hi all,
I have tried to browse the SEQanswers forum for my specific question but could not find anything (which does not mean it does not exist...). I am currently working on an RNASeq experiment involving prokaryotic organisms with partly finished/annotated genomes.

Davis McC (http://seqanswers.com/forums/archive...hp/t-5248.html) has made a very good attempt summarizing the basic steps in RNAseq analysis, but as far as I understood he was describing the analysis for eukaryotes.

Now my question is whether I can employ the same tools, i.e.:

1) Get short reads

2) Map reads against a reference with a short-read aligner like "bwa".

3) Summarize reads using "Rsamtools" in R. This is where I got stuck, I am not sure how to perform this basic operation- any suggestions ?

4) Calculate differential gene expression using an R-based package such as "edgeR" or "DSeq" (I have not tried this either, hints ?)

5) Perform gene-ontology category testing on differentially expressed genes using a package such as "goseq"

I hope I got these very basic steps right and would be greatful for any hints, tips & tricks, experiences using the abovementioned programs on prokaryotes.

Thanks for your help and time !
Cheers
Lars

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NGS - analysis of gene expression data] Machine Learning + RNAseq data	Chuckytah	Bioinformatics	7	03-05-2012 04:16 AM
I need basic help with basic questions re: analysis	rd69	General	3	02-16-2012 04:11 PM
illumina smallRNA adapter sequence for downstram analysis + miRNA analysis steps	ndeshpan	Bioinformatics	2	06-14-2011 10:44 PM
Companies offering NGS data analysis including RNAseq	agseq	Bioinformatics	0	05-05-2011 07:24 AM
PubMed: Initial steps towards a production platform for DNA sequence analysis on the	Newsbot!	Literature Watch	0	03-09-2011 11:40 AM

05-09-2012, 07:27 AM	#1
Muhidini Junior Member Location: Copenhagen Join Date: May 2012 Posts: 1	Basic steps in prokaryotic RNAseq data analysis Hi all, I have tried to browse the SEQanswers forum for my specific question but could not find anything (which does not mean it does not exist...). I am currently working on an RNASeq experiment involving prokaryotic organisms with partly finished/annotated genomes. Davis McC (http://seqanswers.com/forums/archive...hp/t-5248.html) has made a very good attempt summarizing the basic steps in RNAseq analysis, but as far as I understood he was describing the analysis for eukaryotes. Now my question is whether I can employ the same tools, i.e.: 1) Get short reads 2) Map reads against a reference with a short-read aligner like "bwa". 3) Summarize reads using "Rsamtools" in R. This is where I got stuck, I am not sure how to perform this basic operation- any suggestions ? 4) Calculate differential gene expression using an R-based package such as "edgeR" or "DSeq" (I have not tried this either, hints ?) 5) Perform gene-ontology category testing on differentially expressed genes using a package such as "goseq" I hope I got these very basic steps right and would be greatful for any hints, tips & tricks, experiences using the abovementioned programs on prokaryotes. Thanks for your help and time ! Cheers Lars