tximport error
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Joana • 0
Last seen 3 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 • 396 views
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ATpoint ★ 3.4k
Last seen 22 hours 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,

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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

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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


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