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  • Help with subheads featureCounts

    Hi All. I am new to bioinformatics, and am trying to run subReads featureCounts to analyze RNA seq data. I am using the code below, and am in the featureCounts bin directory when I run it:

    ./featureCounts –T 8 –s 1 –t gene -g gene –o /bighome/lastarr/Practice_DA_RNAseq/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/practice6Aligned.sortedByCoord.out.bam/bighome

    Whenever I run this, the manual for featureCounts pops up. I am not sure how to fix this. Thanks so much!
    Last edited by lstarr; 07-24-2022, 05:26 PM.
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