line 1: syntax error near unexpected token `Rsubread

Question

[sehriban.buyukkilic]

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

[Pierre Lindenbaum]

please review all your previous question s that got some answers and validate them if possible . heatmap does not look like good p-value combination methods featurecounts R programmin RNA seq Trimmomatic fastq dump STAR Aligment Running Problem STAR Aligment STAR error MAC Catalina RNA seq STAR Alignment mac trimmomatic problem.

Answer 1

[Pierre Lindenbaum]

how do you invoke this script ?

[sehriban.buyukkilic]

my goodness right, ı was used bash script.R but it should be R CMD BATCH script.R

Thank you so much

[Pierre Lindenbaum]

Please accept the answer so the question is marked solved on the website. To do that, click on the green check mark on the left side of the answer.

[Ram]

Or Rscript script.R