Dear all,

I am using the bioconductor package Rsubread to align reads to a genome:

Rsubread::align(index="output/genome/ref/index/subread/celegans",
                readfile1='output/reads/trimmed/pooled/altadena1.fastq.gz',
                input_format="gzFASTQ",output_format="BAM",
                output_file='output/out2.bam',unique=TRUE,indels=5, nthreads = 8,
                useAnnotation = TRUE, 
                annot.ext = 'output/genome/ref/annotation/celegans.gtf', 
                isGTF = TRUE)

However, this gives me an error:

> rsession: unrecognized option `--gtfFeature'

Whereas this does not give me an error:

Rsubread::align(index="output/genome/ref/index/subread/celegans",
                readfile1='output/reads/trimmed/pooled/altadena1.fastq.gz',
                input_format="gzFASTQ",output_format="BAM",
                output_file='output/out2.bam',unique=TRUE,indels=5, nthreads = 8)

Has anybody come across this problem before?

Thanks a lot.

C.