Installing/Using Feature Counts

Question

[oma219]

Hello,

I know this is a really stupid question but I'm still pretty new to the whole R environment. I'm trying to use featureCounts() so I went into R and installed the rsubread package? When I open the R environment and try to run feature Counts, it tells me that object not found? Do I need to go on and install another package or something? Thanks!

Command in R:

 featureCounts  /home/ubuntu/data/rnaseq/nematostella/venus/alignment/DICDvenus1_STARAligned.out.sam -a /home/ubuntu/data/rnaseq/nematostella/venus/genome/Nemostella_New_Annotation.gff3 > DICDvenus1_counts_featureCounts.txt
Error: object 'featureCounts' not found

Answer 1

[Santosh Anand]

featureCounts  /home/ubuntu/data/rnaseq/nematostella/venus/alignment/DICDvenus1_STARAligned.out.sam -a /home/ubuntu/data/rnaseq/nematostella/venus/genome/Nemostella_New_Annotation.gff3 > DICDvenus1_counts_featureCounts.txt

The problem is that you are trying to run a function in R as a command-line object (like in bash shell). In R, the featureCounts is a function. Run ?featureCounts from inside R to see how it runs. On the other hand, it seems to me that you want to use featureCounts outside R, as a command line. For that, you need to install the subread package from sourceforge http://bioinf.wehi.edu.au/subread-package/ (check Installation from a binary distribution will be easy way if it works)