Question: Creating a count matrix from 8 bam files in R (RNAseq experiment)
gravatar for bananaal1
8 months ago by
bananaal110 wrote:

I have 8 BAM files from an RNAseq experiment (4 different individuals, 2 different tissue types per). The Illumina run was singled-end 50s and we have about 3.2million reads per sample.

I need to know how many counts align to the different parts of the reference genome from each sample identified by tissue type. I am trying to prep my RNAseq data to run bioconductor's DESeq2 protocol but I am stuck getting the count matrix to even start.

I have basically no programming experience; any and all help is welcome and explanations like you are talking to a child would be greatly appreciated.

ADD COMMENTlink modified 8 months ago by Michael Love16k • written 8 months ago by bananaal110
gravatar for Michael Love
8 months ago by
Michael Love16k
United States
Michael Love16k wrote:

Are you at a location that has a bioinformatics facility? You might want to get some help with the bioinformatics. 

Otherwise, read tutorials, e.g.

ADD COMMENTlink written 8 months ago by Michael Love16k
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