featureCounts error???

Question

[Samer]

# get gtf
# wget #https://ftp.ensembl.org/pub/release-110/gtf/mus_musculus/Mus_musculus.GRCm39.110.gtf.gz

input.dir <- "/home/laudy/data/featurecounts/"
setwd(input.dir)

featureCounts -p -O -T -a /input.dir/Mus_musculus.GRCm39.110.gtf -o /input.dir/quants.txt /input.dir/PMN_CTRAligned.sortedByCoord.RD.RG.RC.out.bam

please can someone tell me what's wrong? I tried all the options and he give me the same error:

Error: object 'p' not found
or
Error: unexpected symbol in "featureCounts

Thanks

[rpolicastro]

-T specifies the number of threads, so should have an integer after it.

It's also important to make sure you have the latest version. There were some changes in how the program handles paired-end reads, so to be sure you are doing it correctly check whether you version is current and add the --countReadPairs argument.

[Gordon Smyth]

Subread is implemented both as an Unix program or as an R package. OP seems to be mixing the two versions, and I suspect they have typed a Unix command at the R prompt instead of at the Unix prompt. Typing featureCounts -p etc at the R prompt with Rsubread installed will lead to the object p not found error message.