Using the align() function of the Rsubread package; error: unrecognized option `--gtfFeature'
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4.5 years ago
cristian ▴ 290

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.

rsubread subread ngs next-gen seq alignment • 2.0k views
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