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Hello, I have been trying Salmon software to to quantify my RNA-seq data. I tried the tutorial (which is found here : https://combine-lab.github.io/salmon/gettingstarted/) and everything worked. Then i tried to import the data to Deseq2 but when i read the tutorial, it kinda dazzled me because i am kind of new to R. My question is, when the layout of folders - files - quants.sf is like this "/home/app/Desktop/salmontutorial/quants/DRR016125_quant/quant.sf" , how must be the code in R so i can import them in the correct way-order ? Thanks in advance
i tried this : https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#transcript-abundance-files-and-tximport-input
but the example only uses data from tximportData which is confusing to us new to R. I have multiple quant.sf files from the tutorial so thats my questions, how to load them and process them, because i cant understand from that particular example that has stored data
Go to the tximport vignette first:
vignette("tximport")
from R will work