Problem with MACS2 results

Question

[eilluecaf]

Hi,

I am trying to analyze some ChIPSeq data from Myxococcus xanthus. I tried this and I obtained the following message:

$ callpeak -t /home/eduardo/Documentos/DATOS_TFG/Resultados_Alineamiento/CarD_AntiFLAG_CrecidoLUZ_1.bam -f BAM -g 9.14e+06 -n CarD_AntiCarD_CrecidoLUZ_1

WARNING @ Sun, 29 Apr 2018 19:22:42: 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. 
WARNING @ Sun, 29 Apr 2018 19:22:42: Process for pairing-model is terminated!

Then, I tried this to solve the problem

callpeak -t /home/eduardo/Documentos/DATOS_TFG/Resultados_Alineamiento/CarD_AntiFLAG_CrecidoLUZ_1.bam -f BAM -g 9.14e+06 -n CarD_AntiCarD_CrecidoLUZ_1 --fix-bimodal --extsize 100

The problem is solve but I don't know if the data are reliable. I'd appreciate any guidance. Thanks for your attention.

[ATpoint]

Did you check the data on a genome browser? Are there visible enrichments over the background?

[Devon Ryan]

Is 100 an appropriate fragment size for your data? Presumably you ran it on a bioanalyzer or something...

Answer 1

[Chris Fields]

The error is a hint. A certain number of reliable peaks have to be called for the shift model building step (I think this is ~1-10k). For a smaller genome like M. xanthus this may be an issue as I don't think it's directly adjustable, but you can try adjusting the MFOLD parameter to get more peaks or work around using the --nomodel and --extsize parameters as the error message indicates.