SAF format error

[Ina Hoeschele]

Hi,

I created a SAF file a few months ago without any issues but now I cannot get it to work ... I get this error message:

Error: Line 1 contains a format error. The expected annotation format is SAF.
Error in featureCounts(files = mapped.flist, annot.ext = "/home/inah/RefGTF_38_96/ExonPlus.SAF",  :
  No counts were generated.
Execution halted

I am creating a SAF file because my features are individual bases in specific exons. Below is the code for creating a SAF file:

Start <- seq(from=47395490, to=47395608)
End <- Start
GeneID <- paste("exon1_", Start, sep="")
Chr <- rep("11",length(Start))
Strand <- rep("+",length(Start))
ExonPlus <- data.frame(GeneID=GeneID,Chr=Chr,Start=Start,End=End,Strand=Strand)
write.table(ExonPlus,row.names=FALSE,sep="\t",file="/home/inah/RefGTF_38_96/ExonPlus.SAF")

What is wrong with the format?

Here is how the SAF file looks like:

"GeneID"        "Chr"   "Start" "End"   "Strand"
"exon1_47395490"        "11"    47395490        47395490        "+"
"exon1_47395491"        "11"    47395491        47395491        "+"
"exon1_47395492"        "11"    47395492        47395492        "+"
...

Thanks, Ina

[Yang LIAO]

You should remove the quotation marks in the SAF file -- the columns are delimited by TAB characters hence quotation marks are unnecessary and disallowed in the SAF file.

Also please make sure that the delimiter is TAB, but not SPACE.