Why do you need your own copy of the reference genome?

[CreRecombinase]

Hi, this is a nice piece of software. I was wondering if it would be possible to let the user control where the input data was coming from, instead of just using the ~/.motifscan directory. I already have several copies of hg19 scattered across my machine and it would be great if I didn't have to have to keep an (uncompressed) copy of the reference genome for every bioinformatics tool that I use.

Thanks again!

[hongduosun]

Hi, in the very earlier versions, MotifScan does provide command line parameters for users to specify the path of reference genome file, gene annotation file, motif matrix file... Some users were confused (some people use compressed but others may not, some use one single fasta file but some may prefer one fasta file for one chomosome) and complained about typing these whole paths repeatedly. So MotiScan now put all these files under ~/.motifscan by default and uses a config file ~/.motifscanrc to remember the paths.
But you don't have to put the reference genome under ~/.motifscan. You can move it to any location or merge the contents with an existing copy and then config the path in ~/.motifscanrc
Another workaround is to make a hardlink for the fasta file and this would cost no extra disk usage.
Hope it helps!