Question regarding spike-in normalization

[bartlosz]

Dear authors,

Thank you for providing a great tool to make fast ChIPseq analysis. I was making the analysis using parameters to include spike-in normalization: churros -p 24 /home/ubuntu/input/samplelist.txt /home/ubuntu/input/samplepairlist.txt mm39 /home/ubuntu/Referencedata_mm39 --build_spikein dm6 --Ddir_spikein /home/ubuntu/Referencedata_dm6

Pipeline went smoothly, but I cannot find in commands that were executed any relation with my spike-in (dm6). Therefore I have a question how can I verify if my final results are spike-in normalized?

Best regards!

[bartlosz]

Thank you, but not sure what to do with these files, I am using your docker version of the tool

[rnakato]

Hi bartlosz,

Thank you for using Churros. To enable spike-in mode, please include the --spikein option along with the --build_spikein and --Ddir_spikein options. Churros will then create the bigWig/Spikein/, pdf_spikein/, and spikein_scalingfactor directories, which contain the results of the spike-in analysis.

Since the spike-in command is quite new and hasn't been thoroughly tested, there may be some problems in certain cases. Please let me know if anything seems wrong.

[bartlosz]

Hi,

So in my case I don't have it. I believe spike-in did not work. I am not sure if the step when you download (wget) genome worked correctly for me as I had some warning there.

[rnakato]

Yes, because your command does not contain the --spikein option. Please add it.

churros -p 24 --spikein /home/ubuntu/input/samplelist.txt /home/ubuntu/input/samplepairlist.txt mm39 /home/ubuntu/Referencedata_mm39 --build_spikein dm6 --Ddir_spikein /home/ubuntu/Referencedata_dm6

[bartlosz]

Ah, ok, I see your point now, thank you :)