5

You are right, samples.txt is not generated by Salmon (or any other transcript abundance quantifiers). From documentation, you can find a link to an example of how samples.txt should look like. Note: At the moment, the server is unavailable (I got an Error 503: Service Temporarily Unavailable) - I'd suggest you get directly in contact with the owners / ...


2

By setting type="salmon" you're overriding your settings for things like txIdCol. The various type options (except none) are presets to set things correctly for the output from various programs like salmon or kallisto. If you need to specify custom column names, set type="none". As an aside, if I'm interpreting your question correctly you have only two ...


2

The solution was to use a different library as I expected. It should be library(TxDb.Hsapiens.UCSC.hg19.ensGene). And also, as specified in the question, to remove everything after the dot in the Name column of the quant.sf files.


1

I found this same error as of today using this code: pad.gene.data <- tximport(files = file.list.for.gene.analysis, type = "rsem", txIn = FALSE, txOut = FALSE) dds.gene.level <- DESeqDataSetFromTximport(txi = pad.gene.data, colData = pad.characteristic.data, ...


1

Do your ids in the expression file (from gencode) match up with the gene IDs in the transcript file (from UCSC?) I'm willing to bet that they don't. Stay consistent throughout your process. Either pull down the gencode transcript to gene translations, or do your pseudoalignments to UCSC transcripts.


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