Question: how to set a proper d parameter in MACS
0
gravatar for Lila M
3.2 years ago by
Lila M 810
UK
Lila M 810 wrote:

Hi every body, I'm running MACS2 with this parameters and I have some warning as you can see. They are related to "d" parameter that I've never seen before. Any suggestion?

macs2 callpeak -t file1.BAM -c file2.BAM -g hs -s 36 -m 8 30 -p 0.00001 -B -n proof

WARNING @ Fri, 13 Jan 2017 13:15:07: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! 
INFO  @ Fri, 13 Jan 2017 13:15:07: start model_add_line... 
INFO  @ Fri, 13 Jan 2017 13:15:07: start X-correlation... 
INFO  @ Fri, 13 Jan 2017 13:15:07: end of X-cor 
INFO  @ Fri, 13 Jan 2017 13:15:07: #2 finished! 
INFO  @ Fri, 13 Jan 2017 13:15:07: #2 predicted fragment length is 34 bps 
INFO  @ Fri, 13 Jan 2017 13:15:07: #2 alternative fragment length(s) may be 34,181,256,497 bps 
INFO  @ Fri, 13 Jan 2017 13:15:07: #2.2 Generate R script for model : RECQL5_model.r 
WARNING @ Fri, 13 Jan 2017 13:15:07: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! 
WARNING @ Fri, 13 Jan 2017 13:15:07: #2 You may need to consider one of the other alternative d(s): 34,181,256,497 
WARNING @ Fri, 13 Jan 2017 13:15:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing.
chip-seq macs2 • 1.3k views
ADD COMMENTlink written 3.2 years ago by Lila M 810
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