Hi,
I am trying to run miRDeep2. the subscript make_html.pl uses Rfam to find out more about the sRNAs in question. For this it must creates an bowtie index of the Rfam.fa to map the reads to it.
My miRDeep2 however is located in a directory on a server where it does not have the permissions to create any more directories. Therefore, miRDeep2 can't perform Rfam analysis.
I thought of the following things:
1. Maybe it is possible to provide the path to the index manually by a command line option.
2. Maybe it is possible to change the script and provide a permanent path to the index.
Do you if these options could work? And if yes do you have an idea how? If not do you maybe know another way around this?
I am happy about all suggestions :)
Cheers, Eva
