Content Comparison

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cds
cp -r $BI/ngs_course/listeria_RNA_seq/mapped_data listeria_RNA_seq

Then, skip over the mapping and SAM/BAM conversion, sorting, indexing steps #Create BAM file of mapped reads section below.

Using the R environment for statistical computing

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When you start R later, you will not need to re-install the modules. You can load them with just these commands:

login1$ R
> library("DESeq")
> library("edgeR")

These commands will work for any Bioconductor module!

Create BAM file of mapped reads

Map reads using Bowtie

For RNA-seq analysis we're mainly counting the reads that align well, so we choose to use bowtie. (You could also use BWA or many other mappers.)

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