Convert "Strand" Value from Star aligner output to "SAF" format to extract feature counts with user defined annotation
Star output "SJ.out.tab" has column 4 (column 4: strand (0: undefined, 1: +, 2: -)).
I need to use this and create my annotation file for rsubread's feature counts. A typical user defined annotation looks like the one below. I can convert the 1s and 2s into "+" and "-". How should I handle "0"?
ann <- data.frame(
GeneID=c("gene1","gene1","gene2","gene2"),
Chr="chr_dummy",
Start=c(100,1000,3000,5000),
End=c(500,1800,4000,5500),
Strand=c("+","+","-","-"),
stringsAsFactors=FALSE)
fc_SE <- featureCounts("alignResults.BAM",annot.ext=ann)
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niranjanpandeshwar •
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