I am relatively new to RNA-seq analysis, so I have been following the DESEQ2 tutorial with some sample human data. I attempted to use the "tximeta" function to create a summarized experiment, but I was met with the following error:
library(tximeta) se <- tximeta(coldata) importing quantifications reading in files with read_tsv 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 found matching transcriptome: [ GENCODE - Homo sapiens - release 39 ] useHub=TRUE: checking for TxDb via 'AnnotationHub' snapshotDate(): 2022-04-21 did not find matching TxDb via 'AnnotationHub' building TxDb with 'GenomicFeatures' package Import genomic features from the file as a GRanges object ... Error in download.file(resource(con), destfile) : the 'wininet' method for ftp:// URLs is defunct
It seems that the problem is that 'wininet' no longer works to retrieve the files. I also tried this method:
library("tximport") library("readr") library("tximportData") tx2gene <- read.csv(file.path(dir, "tx2gene.gencode.v27.csv")) Error in file(file, "rt") : cannot open the connection
The .csv file does not exist in my folders, but I'm not sure how to get it. Does anyone know of an alternative method for the wininet so that tximeta will work? Is there any way to tell tximeta to use a different way of opening files? Any advice would be much appreciated.