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Question: Programs used in RNA-seq workflow
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gravatar for cirisarri95
23 months ago by
cirisarri950 wrote:

Good morning everyone, 

I was interested in knowing which programs is the bioconductor package RNA-seq workflow: gene exploratory analysis and differential expression for:

-Quality control

-Mapping

-Counting

-Read Analysis

Thanks everyone!

Regards

ADD COMMENTlink modified 22 months ago • written 23 months ago by cirisarri950
1
gravatar for Michael Love
23 months ago by
Michael Love16k
United States
Michael Love16k wrote:

hi,

I'm not sure I follow your question.

There are a number of R packages used in the workflow.

Every time you see code, such as library("Rsamtools"), that is loading an R package called, "Rsamtools". We describe each package used in each respective section, and when there are multiple options, we describe the one we use as well as provide links to alternatives (counting, differential expression analysis, distance calculation, etc.).

You can just search the page here for "library":

http://www.bioconductor.org/help/workflows/rnaseqGene/

And at the end of the page you can see all the libraries which were loaded throughout the R session, under "other attached packages".

Additionally we describe the use of the STAR read aligner in the workflow, with citation and a link to the STAR aligner software. This software is not an R package, but a standalone tool which is run on the command line.

ADD COMMENTlink written 23 months ago by Michael Love16k

Hi,

Then, if I want to run the whole package workflow, do I need to first run STAR read aligner? Or will it be runned with the rest of the package?

Thanks.

ADD REPLYlink written 22 months ago by cirisarri950
STAR is not actually part of the workflow which is run "live". The live workflow contains only commands in R. We just show you example commands that were used for STAR to make the BAM files used in the workflow. You should prepare the alignment yourself using whatever alignment software you prefer to generate the BAM files.
ADD REPLYlink written 22 months ago by Michael Love16k
0
gravatar for cirisarri95
22 months ago by
cirisarri950 wrote:

Hi,

Thanks for your help. 

Also, for running this workflow, is it set up so that I input data once and it runs the whole process with no more help? Or should I be inputting for each step the data again and again?

ADD COMMENTlink written 22 months ago by cirisarri950
1

You only build the DESeqDataSet (dds) object once, and then the different functions do something and either return the object with new information stored inside of it, or they return a different object.

You'll have to just look at the workflow and follow along. You'll see by the names of the R variables when things are created, when they are modified and when you get a new object as an output of a function.

If you are brand new to R, you may benefit from taking a beginner's R course. I have some R resources collected here: 

http://genomicsclass.github.io/book/pages/resources.html

ADD REPLYlink written 22 months ago by Michael Love16k
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