I'm a Ms Student, and I'm am completely new to galaxy.
Since 4 days I'm am trying to learn the basics, and I've have been able to go from fastq files to a .bed.
I'm using Bowtie2 followed by MACS2 peak calling. I used FastQ groomer on my fastq file in order to use them with bowtie.
You can see my workflow here : http://www.galaxeast.fr/u/vanessa-ueberschlag-pitiot/w/chip-seq-workflow
I mainly use default options.
Now, I wanted to annotate my .bed using homer (still available on the local Galaxy I'm using) but I noted that my .bed file does not contain information about the strand. I know that there is peaks on both strands (I'm using already analyzed data). I do not understand at which point I'm am loosing the strand information, or how I could get it correctly into my bed file
Could please help me ?