Hi, I have problem with my featurecounts script. here is my script. I dont know what is wrong with it. I tried it before it was working without any error but now its giving this error. I check it for syntax but it's seems right to me.
line 1: syntax error near unexpected token `Rsubread'
Any help will me great and useful. Thank you to everyone.
library(Rsubread)
library(BiocParallel)
library(limma)
library(edgeR)
library(stringr
#feature_counts####
bams <- c("SRR20740644.bam",
"SRR20740645.bam",
"SRR20740660.bam",
"SRR20740661.bam")
###counts
counts <- featureCounts(files = bams,
annot.ext = "gencode.v41.primary_assembly.annotation.gtf",
isGTFAnnotationFile= TRUE,
GTF.featureType= c("exon"),
GTF.attrType="gene_id",
useMetaFeatures=T,
countMultiMappingReads=T,
isPairedEnd=FALSE,
nthreads=24)
counts_df <- as.data.frame(counts$counts)
write.table(counts$counts, "/archive/alotaibih/sehribanb/New_rna/d1/Counts/counts.csv", quote = F, col.names = T, sep = "\t")
#calculate fpkm values
z <- DGEList(counts=counts$counts, genes=counts$annotation[,c("GeneID","Length")])
z<- calcNormFactors(z)
RPKM <-rpkm(z)
write.table(RPKM, "/archive/alotaibih/sehribanb/New_rna/d1/Counts/fpkm_values.csv", quote = F, col.names = T, sep = "\t")
done
•
written
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sehriban.buyukkilic •
how do you invoke this script ?
my goodness right, ı was used bash script.R but it should be R CMD BATCH script.R
Thank you so much
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