Error creating DESeq2 Data Set from HTSeq-Count
0
0
Entering edit mode
9 weeks ago

I am trying to run DESeq2 using gene counts generated by HTSeq-Count.

I combine files for different conditions:

directory <- "~/GeneCountFiles/"

WT_Files <- c(
  "P0CTRS3.aligned.sam.genecount",
  "P0CTRS4.aligned.sam.genecount",
  "P0CTRS5.aligned.sam.genecount"
)

KO_Files <- c(
  "P0CTRS1.aligned.sam.genecount",
  "P0CTRS2.aligned.sam.genecount",
  "P0CTRS6.aligned.sam.genecount"
)

I then create the sample table:

sampleTable <- data.frame(
                        sampleName=c(WT_Files, KO_Files), 
                        fileName=c(WT_Files, KO_Files), 
                        genotype=c(rep("WT", length(WT_Files)), rep("KO", length(KO_Files))))

Then I try to create the data set for DESeq2:

library("DESeq2")

ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design = ~genotype)

However, this produces the error:

Error in read.table(file.path(directory, fn), fill = TRUE) : no lines available in input

Any ides why this is happening? I wasn't having any issues just a couple days ago.

htseq-count import deseq2 dataset • 98 views
ADD COMMENT

Login before adding your answer.

Traffic: 1884 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.6