--normalizeUsing RPGC

Question

[Allan]

I am working with deeptools on a cluster. I am trying to run bamCompare using the --normalizeUsing RPGC in the script, but I get an error that Warning! RPGC normalization (--normalizeUsing RPGC) is not supported with bamCompare. Has anyone encountered this before? and how do you dela with it? I am using deeptools 3.5.4

[jordi.planells]

It would be helpful if you include the error message that you are getting.
Have you provided the --effectiveGenomeSize argument?
RPGC normalization requires the genome size, which you can find here
If that's not the case, please provide the error message you encounter.
Cheers,
Jordi

[Allan]

Thanks for the reply, yes I have included the effectiveGenomesize. The error message is

RPGC normalization (--normalizeUsing RPGC) is not supported with bamCompare!

[Allan]

The command I am running is

# Run bamCompare
    bamCompare -b1 "$treatment_bam" -b2 "$control_bam" -o "$output_file" \
            --binSize 10 \
            --numberOfProcessors 25 \
            --extendReads \
            --ignoreDuplicates \
            --samFlagInclude 64 \
            --minMappingQuality 10 \
            --effectiveGenomeSize 1019131369 \
            --normalizeUsing RPGC \
            --scaleFactorsMethod None \
            --centerReads
done

[jordi.planells]

That error message means basically that you can't use RPGC normalization with bamCompare.
However, according to the manual this option should be usable. I would consider other normalization options. Else, contacting deeptools developers?

[Allan]

Thanks. I thought so, though they specify in the documentation that it is possible to use it. I will try and reach out to them.

[Amitm]

Hi, If I remember correctly, you cannot turn scaling off, if you are using the normalisation method 'RPGC'. If you leave --scaleFactorsMethod at default setting, then you could use 'RPGC'. The documentation doesn't make this explicit, but I had received the same error message and I different parameter settings.

[Allan]

thanks so much for the response. I will give it a try

[Allan]

If it may help, I am using a non model organism. A termite species Cryptotermes secundus

Answer 1

[Devon Ryan]

You can't use RPGC normalization with bamCompare, simply use something else. Yes it's rather annoying that it's listed in the documentation as an option. This is due to using the same command-line generation code across multiple tools. Probably someone should put in a switch to just have that one excluded, which would prevent this.