macs2 output r file not generated

Question

[mavy]

Hello

I am working on chipseq data, for peak calling I used macs2 and following command. As an output its generating the bdg file but no R file is being generated

Kindly suggest what am I doing wrong.

macs2 callpeak \
  -t _unique_rmdup_sampled.bam \
  -c INPUT_unique_rmdup_sampled.bam \
  --gsize 3.0e9 \
  --broad \
  --broad-cutoff 0.1 \
  --nomodel \
  --extsize 125 \
  --bdg \
  -n output \
  --outdir chip_seq/chip_workflow/results/macs/

Any help is appreciated

Answer 1

[jared.andrews07]

It will not output that file with --nomodel set.

[mavy]

Thanks for your response ! but if I don't use --nomodel the following error comes

ERROR: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. 

Any suggestion on how to produce the graphs then??

[jared.andrews07]

Well, you can either continue without the model set or follow the error suggestions to increase the MFOLD range. I'd be concerned about data quality if it is calling zero peaks while building its own model (or very few if the model is ignored).