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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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Q: No model.r files generated #281

Open chaimol opened 5 years ago

chaimol commented 5 years ago

Hi. I ran execute MACS2 as below: $macs2 callpeak -t ID1_sort.bam -c HALO_sort.bam -g 2.1e9 -B -f BAMPE -n ID1-HALO --outdir macs2-out 2> err-macs2.log I have the following outputs:

ID1-HALO_control_lambda.bdg  ID1-HALO_peaks.xls    ID1-HALO_treat_pileup.bdg  ID1-Y_peaks.narrowPeak  ID1-Y_summits.bed
ID1-HALO_peaks.narrowPeak    ID1-HALO_summits.bed  ID1-Y_control_lambda.bdg   ID1-Y_peaks.xls         ID1-Y_treat_pileup.bdg

I realize that there is supposed to be model.r output as well but it is missing. Any idea how I could generate this file? The version of macs2 2.1.1.20160309 .

rushikapandya commented 5 years ago

Hello,

I am facing the same issue. I am using macs2 2.1.2. If I run macs2 with the flag -f BAMPE, model.R is not generated. However, when I run without the -f flag and on a bam file, macs2 generates a model.R file. I want to be able to generate the model.R file for my data but i am not sure what the bug is here? I'd really appreciate your help.

taoliu commented 5 years ago

In BAMPE mode, there is no need to estimate fragment lengths since the actual insertion length for each read pair will be considered. That's why there is no model.R generated.