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saddamhusain77
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@saddamhusain77-19420
Last seen 5.6 years ago
I am trying to figure out how to use IsoformSwitchAnalyzeR on Salmon quantification. I'm really stuck at the very beginning. I have not been able to import the data. Below is the code I am using-
getwd()
[1] "/Users/saddamhusain/Desktop/salmon_isoswitch"
salmonQuant <- importIsoformExpression(
parentDir = system.file("salmonQuant", package="IsoformSwitchAnalyzeR")
)
Step 1 of 3: Identifying which algorithm was used...
Error in dirList[sapply(dirList, FUN = function(aDir) { :
invalid subscript type 'list'
salmon_isoswitch is a directory that contains salmonQuant subdirectory that in tern contains four independent subdirectories for each sample.
Any help will be appreciated.
With this code-
Step 1 of 3: Identifying which algorithm was used...
Error in importIsoformExpression("salmonQuant") : No directories of interest were found
Even though .txt files of count data are there.
Can you work through the example data successfully first?
https://bioconductor.org/packages/release/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html
I suggest reading the section in the longer workflow called ' Importing Data from Kallisto, Salmon, RSEM or StringTie'. It is pretty straightforward, I use this command, where this is simply the directory my salmon folders are in:
salmonQuant <- importIsoformExpression( parentDir = "C:/Users/chris/Desktop/isoswitcher/NewTranscriptomePEACbaseline/stringtie.salmon.v26/", addIsofomIdAsColumn = TRUE )
Thank you chris for the response. Yes, I can work through the example data smoothly but still getting the error with my data.
Step 1 of 3: Identifying which algorithm was used...
Error in importIsoformExpression(parentDir = "/Users/saddamhusain/Desktop/salmon_isoswitch/") :
No directories of interest were found
salmonisoswitch folder contains four different folders named as "helc1" "helc2" "helt1" and "hel_t2" each of which contains respective quant.txt file.
OK, I think there is something different with your salmon output directories. I don't know what that is. Make sure your output directories contain all the files and folders normally outputted by salmon into a directory per sample.
If you are sure your output directories are as normal (they match example ones), then ask here for more help, https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues.
I got quantification and gene quantification output from salmon ( v-0.13.1). I have done differential expression analysis on quantification files so I suppose same files should work out on isoformswitchanalyzer. Thanks for the suggestion. I have raised the same issue on GitHub too and am following it.
Try doing some example read alignments and then just trying to input the directory into R. I am having no problems with it, I'm using the latest version of salmon and not changing the output folder files and structure at all afterwards.
Thanks Chris, yeah, I will try to figure it out.