I want to reproduce the experimental results of this article:https://www.nature.com/articles/nprot.2013.099#Abs1
but after download sra files with this code↓：
sri = read.csv("SraRunInfo.csv", stringsAsFactors=FALSE)
keep = grep("CG8144|Untreated-", sri$ LibraryName)
sri = sri[keep,]
fs = basename(sri$download_path)
for(i in 1:nrow(sri))
download.file(sri$download_path[i], fs[i])
I got some files with extensions .2 such as SRR031708.2
By the way, my SraRunInfo.csv was download by send to→file→runinfo in the NCBI page. Please tell me how to fix this problem. Thank you very much.
first picture is the SraRunInfo.csv in the article
second one is what in the SraRunInfo.csv I download
That is how the R basename function works:
basename("a/b.2")
[1] "b.2"
from the help
basename removes all of the path up to and including the last path separator (if any).
Thank you very much, but my download path in SraRunInfo.csv which download from NCBI is different from the article, I think it is the problem
Thank you very much!
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Which SRA accession numbers are you working with?
SRA accession is SRP001537