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how to install macs and use it

Sorry if I'm asking a stupid question.

I have chip-seq raw data, with fastq.gz format file, and I want to call peaks firstly. I have python installed in my computer.

Python 2.7.8 (v2.7.8:ee879c0ffa11, Jun 29 2014, 21:07:35)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
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How can I install MACS and how to use it? I went to MACS website, and I don't quite understand the install guide.

Thank you!

chip-seq
• 6,579 views • link
updated by Ram Ram • written by catherine catherine

You'll probably want to check out galaxy, since I gather you're quite new to this sort of thing.

• 2 views • link
written by Devon Ryan Devon Ryan

BTW, you'll need to align the reads before you can use MACS. For that, a tool like bowtie2 or bwa will work.

• 2 views • link
updated by Ram Ram • written by Devon Ryan Devon Ryan

3 answers

https://github.com/taoliu/MACS/blob/macs_v1/INSTALL.rst

You can download the source distribution and uncompress the distribution. Then move into the directory and run python setup.py install

• 2 views • link
written by Ashutosh Pandey Ashutosh Pandey

I recommend using virtualenv to keep your macs installation isolated from the rest of your system: virtualenv - running Python based software in isolation

As Devon Ryan said you'll need to map your reads first. A good general review of running MACS2 was recently published: http://www.ncbi.nlm.nih.gov/pubmed/?term=24743991

• 0 views • link
updated by Ram Ram • written by Ian Ian

Try making sure that your python version is compatible with your macs program and examine the instructions for python setup.py install

• 0 views • link
updated by Ram Ram • written by NHEJ NHEJ

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