Hi,
I am trying to run a count matrix using featurecounts but it is showing me 'invalid parameter' error with the file path to my bam files. I have checked and the files exist along with executable permissions. Here is my code:
$feature_counts -p -T 8 -a $gene_ann -o $count_out/count_matrix.txt $bam_dir/*_aligned.bam
ERROR: invalid parameter
Could someone please help me with that?
Please check this link for the parameters settings. You have missed some of the parameters.
Thank you for the link! I had a look and updated the script:
# Run featureCounts to generate a count matrix
$featurecounts -p -O -M -T 8 -a $gene_ann -F GTF -t exon -g gene_id -o $count_out/count_matrix.txt $bam_dir/*.bam
However, it is still showing as : ERROR: invalid parameter:/path/to/file/SRR7008461_aligned.bam'
If you are using -p for paired end data then you should also use
--countReadPairs Count read pairs (fragments) instead of reads. This option
is only applicable for paired-end reads.
I always list the BAM files individually with a space in between names. As Gordon Smyth said below the wild card does not work (*.bam).
Make sure all your variables expand to generate correct paths. It is odd to use a variable for a program name.
One obvious issue is that the software is called featureCounts rather than feature_counts. Is feature_counts perhaps a customized script on your own system?
I don't see anything in the featureCounts documentation that it accepts wild characters in file names.
Sorry, I think there is a confusion. I declared the path to where the featurecounts software is and called that variable feature_counts earlier on in the script. So, I was just calling that in this part of the script. I hope this makes more sense :)
This is my first time doing rnaseq analysis so a bit confused.
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