Question: FastQ to annotated MACS Peaks
gravatar for giroudpaul
3.5 years ago by
giroudpaul0 wrote:


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 :

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 ?

Thanks you,


strand bed bowtie macs • 1.6k views
ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson25k • written 3.5 years ago by giroudpaul0
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


ChIP-seq peak data cannot be accurately assigned a strand because the reads are DNA, meaning that it is technically an unstranded data type at the stage where peaks are called. It can however be annotated against stranded data - perhaps this is where peaks were assigned a strand in your reference data?

Homer will accept various stranded inputs, but this would not be from a ChIP-seq experiment. The findPeaks function of Homer might be the best choice for peak calling (instead of MACS2). This function and the preparatory functions are included in Galaxy wrapped Homer repository from the Tool Shed.

More about how to analyze data with Homer is here:

Hopefully this helps! Best, Jen, Galaxy team

ADD COMMENTlink written 3.4 years ago by Jennifer Hillman Jackson25k
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