Question: Error : Salmon tximport to DESeq2
0
gravatar for saddamhusain77
9 months ago by
saddamhusain770 wrote:

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.

deseq2 tximport • 374 views
ADD COMMENTlink modified 9 months ago by Michael Love25k • written 9 months ago by saddamhusain770
Answer: Error : Salmon tximport to DESeq2
0
gravatar for Michael Love
9 months ago by
Michael Love25k
United States
Michael Love25k wrote:

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

ADD COMMENTlink written 9 months ago by Michael Love25k

Thank you Michael for the quick response, I will go back and check vignette. I have ran the salmon on galaxy platform and it generated tabular files instead of .sf. is it even possible to import tabular files by tximport?

ADD REPLYlink written 9 months ago by saddamhusain770
1

Now that I can see the code more clearly, it looks like you have NA values in your tx2gene table. Try removing those rows first.

ADD REPLYlink written 9 months ago by Michael Love25k

It worked, Thank you for your time.

ADD REPLYlink written 9 months ago by saddamhusain770
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