Using Zagros & understanding its results

Question

[anu014]

Hi everyone,

I am trying this new tool called Zagros for motif prediction. It consists of 3 sub-programs. I'm stuck with one of it called 'extractDEs'. It tells me to use native output format for bowtie ,so I tried '.map' files but it didn't work. Then I tried 'rmap' alignment tool result ,ie. BED file still I was unable to get it working. I used following commands :

/softwares/zagros-1.0.0/bin/extractDEs -m rmap -t hCLIP -o input.des -r /clip-seq/mapped_locations.bed -v   

home/anupriya/softwares/zagros-1.0.0/bin/extractDEs -m bowtie -t hCLIP -o input.des -r /home/anupriya/clip-seq/mapped_reads.map -v

And can I use bowtie2 with this tool?

Link for the tool : http://smithlabresearch.org/software/zagros/

Thanks in advance!