Question: MACS2 input not recognized by tool
0
gravatar for virlana.shchuka
24 months ago by
virlana.shchuka0 wrote:

Hi all,

I've been using Galaxy to analyze my ChIP-seq data, and have managed to get the program to call narrow peaks when I uploaded my bam files. I want to call broad peaks as well though, and the bedgraph files I upload onto the Galaxy disk are not being recognized by the MACS2 bdgbroadcall program. Am I uploading the files to the wrong spot, or otherwise missing something very obvious?

Thanks in advance!

ADD COMMENTlink modified 24 months ago by Jennifer Hillman Jackson25k • written 24 months ago by virlana.shchuka0
0
gravatar for Jennifer Hillman Jackson
24 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Double check the datatype assignment and adjust as needed. How to: https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

Thanks, Jen, Galaxy team

ADD COMMENTlink written 24 months ago by Jennifer Hillman Jackson25k

Hi Jennifer,

Thanks for your quick reply. The issue is that when I upload the bedgraph files, the bdgbroadcall "MACS score in bedgraph" section says "no bedgraph dataset available". The files I'm uploading are definitely bedgraph files, so I don't think it's a format issue. Does the MACS tool need to generate a bedgraph from a bam file itself, which it can then use as input in this program (i.e. externally uploaded files are not recognized)?

ADD REPLYlink written 24 months ago by virlana.shchuka0

Is the datatype metadata attribute assigned as bedgraph for the input datasets? And these not found by the tool form? This is distinct from confirming the actual format. The link above explains how to assign or modify datatype.

I cannot reproduce this independently with inputs having the datatype assigned at http://usegalaxy.org. Are you working somewhere else?

ADD REPLYlink modified 24 months ago • written 24 months ago by Jennifer Hillman Jackson25k
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