assign Ensemble gene ids to transcripts

[HadrienG]

in the RNA seq tutorial in this code block

txdb <- makeTxDbFromGFF("chr22_genes.gtf")
k <- keys(txdb, keytype = "GENEID")
tx2gene <- select(txdb, keys = k, keytype = "GENEID", columns = "TXNAME")
head(tx2gene)

GENEID and TXNAME should be swapped

[TheMuffinMan563]

This is a poor tutorial with many reference file not being provided. Where can we get chr22 fasta files, what's the samples.txt suppose to contain in "samples <- read.table("samples.txt", header = TRUE)", what's the mapping rates for salmon quant.

[HadrienG]

Both the chr22 fasta file and the sample.txt file are in the toy_rna.tar.gz archive.

Thank you for your constructive feedback 😊

[TheMuffinMan563]

Yeah sorry later on I realized the manual download link for FASTQ doesn't have it whereas curl via curl -O -J -L https://osf.io/7zepj/download has all the necessary elements. I didn't know they would be different.