Closed cartal closed 7 years ago
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
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:
"~/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