Question: Need help with "MACS" tool--program setting
gravatar for zhhxu9
3.4 years ago by
zhhxu90 wrote:


I have a question about running MACS tool for my chip-seq data to call the peaks for the transcription factor binding site.

1. My data is pair-end sequenced. I have already upload the two FASTQ datasets R1 and R2 into galaxy, converted into the right format and run the Bowtie tool for mapping.

2. After mapping, I got one SAM dataset from the two FASTQ dataset. 

3. When I want to run MACS tool, under the "Paired End Sequencing" option, if I select "single end", the SAM dataset in history can be recognized; however, if choose "paired end", it asks for the elandmuti format. and asks for two ChIP-seq Tag files.

4. I want to know should I choose single-end or paired-end?

5. Because my sequencing is paired-end sequencing, is that correct if I should choose single-end? 

6. If I choose paired-end, how can I get the elandmuti format dataset and what are the two files the tool asks stand for? Are they the datasets from the two biological replication?

7. What is the tag size stands for?

I have no experience in bioinformatics, sorry for those stupid questions. and I appreciate for the kind reply.




Tool name: MACS
Tool version: 1.0.1
Tool ID:
ToolShed URL:


macs • 1.1k views
ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson23k • written 3.4 years ago by zhhxu90
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hi Zhenhua,

MACS on the public Main Galaxy instance is used mainly with single end data (v1 No tools on Main produce ENLAND format. To understand it better, a description is included in the lastest MACS documentation in the next link befow). This post at seqanswer has some community advice including links to more resources:

These should address most your questions in a more specific way than quick answers that will not apply to all situations (and some are related). Getting the big picture will help things fall into place. The tutorial/learn link at the end of this post will help even more.

So that you and others know, there is an updated version v2 that we plan to add to Main and it is already in the Tool Shed for use in a production local or cloud Galaxy.

SICER is your other option on Main (and also in the Tool Shed). It technically is designed for single-end data, but this post to the SICER google group has a reply from the tool author that explains how to input paired-end data.!topic/sicer-users/E3y1PimR96U
Reviewing other posts here is a great way to learn about SICER or you can of course join the group and ask specific tool-related question. 

We also have many Galaxy-based tutorials that include MACS. Both in the Shared resources on Main and in our wiki under "Learn" Most use single-end data, but a great deal of the scientific/usage/troubleshooting recommendations should work across inputs. Be sure to explore the custom google searches in the link above. 

Hopefully this helps you find your way! Everyone started new at some point, so please let us know if we can still help with using the tool in Galaxy if you have questions after learning a bit more about it from the above.

Best, Jen. Galaxy team

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Jennifer Hillman Jackson23k
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