Error: all(file.exists(files)) is not TRUE

[cartal]

Hi

I'm working with some Salmon files using mouse RNA-Seq. I have followed the steps of the vignette and it seems to work, until I reach the tximport step when I run the following command:

txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene, reader = read_tsv)

I get the following error:

Error: all(file.exists(files)) is not TRUE

I am not sure if this is an issue with tximport or with my own data.

My tx2gene looks like this:

TXNAME,GENEID
ENSMUSG00000064372,mt-Tp
ENSMUSG00000064371,mt-Tt
ENSMUSG00000064370,mt-Cytb
ENSMUSG00000064369,mt-Te

and my files looks like this:

                                                                                                   sample_1

"/Documents/data/samples/deconv//salmon/sample_1/quant.genes.sf"
sample_2
"/Documents/data/samples/deconv//salmon/sample_2/quant.genes.sf"
sample_3
"~/Documents/data/samples/deconv//salmon/sample_3/quant.genes.sf"

Thanks in advance for pointing out to a solution or a glaring error from my side.

Regards

[mikelove]

hi,

As this software moved to Bioconductor, the appropriate place for asking software questions is: http://support.bioconductor.org

But I can tell you, your problem here is that you need to specify a correct path to your files. all(file.exists(files)) is not TRUE means that the paths in files are not correct.

Please post any follow up or future questions to http://support.bioconductor.org