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Question: MACS2 input not recognized by tool
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gravatar for virlana.shchuka
2.2 years ago by
virlana.shchuka • 0
virlana.shchuka • 0 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!
input metadata datatype macs2 chip-seq • 775 views
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modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by virlana.shchuka • 0
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gravatar for Jennifer Hillman Jackson
2.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 2.2 years ago by virlana.shchuka • 0

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 REPLY • link modified 2.2 years ago • written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k
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