Hi, I am trying to tximport Salmon output from the Galaxy, which is a quantification file in tabular format (instead of .sf format?). I have followed the Users manual of DESeq2 to tximport but got the error at txi step.

files1 <- list.files( pattern = ".txt",full.names = TRUE)

names(files1) <- paste0("samples", 1:4)

all(file.exists(files1))

[1] TRUE

head(tx2gene)

  TXNAME    GENEID

1 uc001aaa.3 100287102

2 uc010nxq.1 100287102

3 uc010nxr.1 100287102

4 uc001aal.1 79501

5 uc001aaq.2 NA

6 uc001aar.2 NA

txi <- tximport(files1, type = "salmon", tx2gene = tx2gene)

reading in files with read_tsv

1 2 3 4

summarizing abundance

summarizing counts

summarizing length

Error in summarizeToGene(txi, tx2gene, varReduce, ignoreTxVersion, ignoreAfterBar,

all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE

In addition: Warning messages:

1: In rowsum.default(abundanceMatTx, geneId) : missing values for 'group'

2: In rowsum.default(countsMatTx, geneId) : missing values for 'group'

3: In rowsum.default(abundanceMatTx * lengthMatTx, geneId)

missing values for 'group'

4: In names(aveLengthSampGene) == rownames(lengthMat)

longer object length is not a multiple of shorter object length

Samples file contains my sample information in 4x4 dim. Any suggestions, advice would be appreciated, Thanks in advance.

Check the vignette and help files for example usage. files should point to quant.sf files produced by Salmon.