using rf-count with bowtie-index

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EmiWe

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Oct 16, 2019, 12:00:12 PM10/16/19
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Hello, 
it seems that I am not using the right command for counting the reads.
I do not have a transcriptome reference so I am using the following in order to use bowtie-index:

$ ./rf-count -bi plasmid-index/plasmids map.bam


And then this error jumps up:


[!] Error: Invalid option. Please check the help



What am I doing wrong?

Thank you for your help!!!


Emilia


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