tximport error
Entering edit mode
Joana • 0
Last seen 6 months ago
United Kingdom


I am trying to create a txi list with transcript data from running Salmon. I have created a tx2gene file with 2 columns with protein product and locus tag taken from NIH. However i am getting the following error when running the command for tximport

txi <- tximport(files, type="salmon", tx2gene=tx2gene)


reading in files with read_tsv 1 Error in tximport(files, type = "salmon", tx2gene = tx2gene) : all(c(abundanceCol, countsCol, lengthCol) %in% names(raw)) is not TRUE

Any help would be appreciated. Thanks JD

tximport r • 915 views
Entering edit mode
ATpoint ★ 4.2k
Last seen 11 minutes ago

Has the salmon output been modified in some way? Can you show a head of any of the quant.sf files in the salmon output of any sample? By the way, with protein product and locus tag taken from NIH -- what does that mean? The file should be transcript identifier in column 1 and gene identifier in column 2,

Entering edit mode

Thank you for getting back to me. I am new at RNAseq analysis so not sure if i am doing it the right way.

In order to do get the transcriptome file to run salmon i took the fasta file with coding sequences from this NIH https://www.ncbi.nlm.nih.gov/nuccore/197361212?report=fasta and attached an image of the file head of transcriptome fileand to get the list of transcript -> gene i got the 2 columns of Protein Product (transcript) and Locus tag (gene id) from here https://www.ncbi.nlm.nih.gov/genome/browse/#!/proteins/152/299238%7CSalmonella%20enterica%20subsp.%20enterica%20serovar%20Paratyphi%20A%20str.%20AKU_12601/ and an image form R is here tx2gene file from R.

The only thing i changed in the quant.sf files was the name of the transcripts (first column) as they came out as the full name from transcriptome file - everything after '>' and so i just shorten them to match the transcript name column of tx2gene file.

Could you please tell me if you can tell where i went wrong on this?

Thank you once more

Entering edit mode

tximport reads in the files as output by Salmon. If you manually changed the files and their headers you will have to tell tximport your new columns names. See ?tximport


Login before adding your answer.

Traffic: 666 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6