Hello! I am trying to run featureCounts v1.6.2 to use for DESeq2. I am running the following command:

./featureCounts -T 8 -s 2 -t gene -o /bighome/lastarr/Practice_DA_RNAseq/featureCounts/input.counts.txt -a /bighome/lastarr/c_elegans.PRJNA13758.WS285.canonical_geneset.gtf /bighome/lastarr/Practice_DA_RNAseq/results/practiceAligned.sortedByCoord.out.bam /bighome/lastarr/Practice_DA_RNAseq/results/practice2Aligned.sortedByCoord.out.bam /bighome/lastarr/Practice_DA_RNAseq/results/practice3Aligned.sortedByCoord.out.bam /bighome/lastarr/Practice_DA_RNAseq/results/practice4Aligned.sortedByCoord.out.bam /bighome/lastarr/Practice_DA_RNAseq/results/practice5Aligned.sortedByCoord.out.bam /bighome/lastarr/Practice_DA_RNAseq/results/practice6Aligned.sortedByCoord.out.bam

When I do this, the error message ERROR: invalid parameter: '/bighome/lastarr/Practice_DA_RNAseq/results/practiceAligned.sortedByCoord.out.bam' pops up. I do not know why, as this is the correct pathway to the file. How can I fix this? Thanks!

It's neither related to DESeq2 or Bioconductor, so in the future better post this at something like biostars.org.

Anyway, are these bam files in the command spanning multiple lines? Hardto tell because you do not use markdown to wrap your code chunk. Is there a newline after gtf? If so then indicate that with \ before every newline. Or make your life easy and use *.bam given that you want to count all bam files n that folder.

featureCounts (...options...) path/to/folder/*.bam

featureCounts (...options...) \
path/to/bam1.bam \
path/to/bam1.bam \
(...) \
path/to/bamN.bam