Hi Folks,
I ran Salmon through (usegalaxy.org), saved the output files in separate folders as expected by wasabi.
I just had a problem with prepare_fist_for_sleuth(sfdirs). I have never used wasabi to convert files before, but have used Sleuth to analyze Kallisto outputs, and was interested in comparing Salmon outputs through Sleuth because of the --gcbias and --seqbias options that Salmon has.
Error in setnames(quant, c("target_id", "length", "tpm", "est_counts")) :
Can't assign 4 names to a 5 column data.table
Is the function having trouble converting the 5 column Salmon quant.sf file to the 4 column sleuth-ready file?
Here are the commands I ran:
source("http://bioconductor.org/biocLite.R")
biocLite("COMBINE-lab/wasabi")
library(wasabi)
files <- file.path(dir, "salmon")
sfdirs <- file.path(files, c("S2", "S3", "S4", "S5", "S7", "S8"))
all(file.exists(sfdirs))
salmon <- prepare_fish_for_sleuth(sfdirs)
Hi Folks, I ran Salmon through (usegalaxy.org), saved the output files in separate folders as expected by wasabi. I just had a problem with prepare_fist_for_sleuth(sfdirs). I have never used wasabi to convert files before, but have used Sleuth to analyze Kallisto outputs, and was interested in comparing Salmon outputs through Sleuth because of the --gcbias and --seqbias options that Salmon has.
Error in setnames(quant, c("target_id", "length", "tpm", "est_counts")) : Can't assign 4 names to a 5 column data.table
Is the function having trouble converting the 5 column Salmon quant.sf file to the 4 column sleuth-ready file?
Here are the commands I ran: source("http://bioconductor.org/biocLite.R") biocLite("COMBINE-lab/wasabi") library(wasabi) files <- file.path(dir, "salmon") sfdirs <- file.path(files, c("S2", "S3", "S4", "S5", "S7", "S8")) all(file.exists(sfdirs)) salmon <- prepare_fish_for_sleuth(sfdirs)
Thanks for your help!
Laryssa