Unused argument in cn_salmon

[rajinder4489]

I am trying to run CellNet for RNA-Seq data locally but at the step 6.B mentioned in your Nature protocols paper, I am having an error unsed arguiment for 'geneTabfname'.

expList<-cn_salmon(stQuery, refDir="ref/", salmonIndex=iFileHuman, salmonPath=pathToSalmon, geneTabFname="geneToTrans_Homo_sapiens.GRCh38.80.exo_Jul_04_2015.R")

Error in cn_salmon(stQuery, refDir = "ref/", salmonIndex = iFileHuman, : unused argument (geneTabFname = "geneToTrans_Homo_sapiens.GRCh38.80.exo_Jul_04_2015.R")

Then just to check I tried running it without geneTabfname, all other steps in it ran but then it gives an error that the file not found

expList<-cn_salmon(stQuery, refDir="ref/", salmonIndex=iFileHuman, salmonPath=pathToSalmon)

In readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file 'ref//geneToTrans_Mus_musculus.GRCm38.80.exo_Jun_02_2015.R', probable reason 'No such file or directory'

I checked the help document and also the cn_salmon function file from the bin but couldn't find any help there as well

I also tried giving the full path for the file but it made no difference

Another point to make here, thoiugh I am using the Human example but I get the file not found for Mus musculus

[pcahan1]

Can you see what happens when you change "geneTabFname" to "geneTabfname" to match the function definition?

[rajinder4489]

Hi Patrick
Thanks for your response
Yes it worked with this