MACS2 and single file for analysis

Question

[Morris_Chair]

Hello everyone, I am new to ChIP-seq and I want to reproduce an analysis from a paper . In SRA they loaded only one file, the one used for the ChIP experiment without any control or MOCK files, then I was told that it is possible to analyze only one file so I want to ask you if it's ok to use this command line without input as first step:

macs2 callpeak -t ChIP.bam 
    -f BAM -g 1.3e+8 
    -n Nanog-rep1 
    --outdir macs2

Thank you

[ATpoint]

Yes, this command is possible. If you want to know how the tool estimates the background levels check the original MACS paper (keyword is local lambda). Still, technically possible does not mean that this is a good experiment. Depending on antibody quality you might get lot of unspecific binding that a proper IgG control would've eliminated but if this is what they uploaded you can go ahead with it.

[Morris_Chair]

Hi ATpoint,

I run it and I got different files including an excel file for the peaks location. Next step will be to visualize/normalize this peaks, can you suggest tool for that? preferably that run with Studio

thanks

[ATpoint]

If you have only one sample, what do you want to normalize against? What is Studio, RStudio?

[Morris_Chair]

I read somewhere that when there is only one file MACS is able to apply a normalization in order to distinguish noise and peaks so it's not for this case. I will need to normalize against the input others files.

yes it was a typo, I meant Rstudio

tnx

[ATpoint]

But you said you have no controls? If you do, include them into the macs command with -c. Beyond that, I do not see what one could do with only a single sample. For visualization, check bamCoverage from deeptools. Also check online for ChIP-seq tutorials, as this is all part of standard workflows.

[Morris_Chair]

I am doing things in parallel sorry for the confusion:D ok, I have only one file and I can still visualize significant peaks which is already good,

I thought deeptools could run only with python,

tnx

[ATpoint]

I thought deeptools could run only with python

Yes. Can be run from the command line like most tools.