FeatureCounts Invalid Parameter Error

Question

[Jamie]

Hello! I'm trying to use featureCounts, and it keeps on giving me this error:

ERROR: invalid parameter: 'SRR11860547.bam'

I'm pretty new at using featureCounts, so I have no clue what is wrong. I've tried changing the directory and location of the file, but it keeps on giving me the same error. Does anyone know what this error could mean?

This is my main code by the way:

featureCounts -a Homo_sapiens.GRCh38.110.gtf -o quants/SRR11865047_featurecounts.txt SRR11860547.bam

Thank you so much!

[sansan96]

Hello,

It looks like your data is paired-end, correct? If so you need to add the argument: -p --countReadPairs

Example:

featureCounts -p --countReadPairs -t exon -g gene_id -a annotation.gtf -o counts.txt mapping_results_PE.bam

[ATpoint]

Can you add a screenshot from the terminal when this error occurs, because I do not see anything wrong in the command. Maybe in the screenshot one sees odd spaces or something like this.

[Ram]

Please push users towards copy-pasting the error instead of using screenshots.

[ATpoint]

There is a good reason I do so if you read my request again, thank you.

[Ram]

Even so, I think the output to something like echo <command> | cat -te will be more insightful than a screenshot. What do you think?