NeoLoopFinder for Micro-C

[PinpinSui]

Hi Xiaotao,

Thank you very much for this wonderful tool. Does NeoLoopFinder apply to MicroC data? And "uniform" should be selected for "-e" parameter? Thank you,

Pinpin

[PinpinSui]

Hi Xiaotiao, When I use -e uniform for 500M Micro-C contactmatrix, The following error occurred. What is the possible reason? The commond is as follows: calculate-cnv(0.4.3-r2) -H matrix.mcool::resolutions/16000 -g hg38 -e uniform --output mc_16kb.CNV-profile.bedGraph Thank you, Pinpin

[XiaoTaoWang]

Hi Pinpin, this seems just a warning message, did you get any results in the end?

[PinpinSui]

Hi Xiaotao,

Just a log file genarated: cnv-calculation.log and no other output. The content within the log file is as follows.

rpy2.rinterface_lib.embedded INFO @ 04/03/23 08:03:08: Default options to initialize R: rpy2, --quiet, --no-save rpy2.rinterface_lib.embedded INFO @ 04/03/23 08:03:09: R is already initialized. No need to initialize. root INFO @ 04/03/23 08:03:11: Calculate the 1D coverage from Hi-C matrix ... root INFO @ 04/03/23 08:03:26: Load GC content ... root INFO @ 04/03/23 08:04:08: Load mappability scores ... root INFO @ 04/03/23 08:04:50: Count the number of cut sizes for each bin ... root INFO @ 04/03/23 08:05:23: Filter out invalid bins ... root INFO @ 04/03/23 08:05:23: Done root INFO @ 04/03/23 08:05:23: Fitting a Generalized Additive Model with log link and Poisson distribution ... rpy2.rinterface_lib.callbacks WARNING @ 04/03/23 08:05:29: R[write to console]: Error in smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) : A term has fewer unique covariate combinations than specified maximum degrees of freedom

Traceback (most recent call last): File "/data/suip/software/anaconda3/envs/neoloop/bin/calculate-cnv", line 164, in run gam = mgcv.gam(fomula, family=stats.poisson(link='log')) File "/data/suip/software/anaconda3/envs/neoloop/lib/python3.10/site-packages/rpy2/robjects/functions.py", line 208, in call return (super(SignatureTranslatedFunction, self) File "/data/suip/software/anaconda3/envs/neoloop/lib/python3.10/site-packages/rpy2/robjects/functions.py", line 131, in call res = super(Function, self).call(*new_args, *new_kwargs) File "/data/suip/software/anaconda3/envs/neoloop/lib/python3.10/site-packages/rpy2/rinterfacelib/conversion.py", line 45, in cdata = function(args, **kwargs) File "/data/suip/software/anaconda3/envs/neoloop/lib/python3.10/site-packages/rpy2/rinterface.py", line 817, in call raise embedded.RRuntimeError(_rinterface._geterrmessage()) rpy2.rinterface_lib.embedded.RRuntimeError: Error in smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) : A term has fewer unique covariate combinations than specified maximum degrees of freedom

When I use higher 32kb resolution, I can be run successfully.

Thank you, Pinpin

[iagooteroc]

Hello. This also happens to me with 25kb resolution and -e uniform

calculate-cnv -H Micro-C_H2087_E0016_balanced.mcool::resolutions/25000 \
-g hg38 -e uniform --output Micro-C_H2087_E0016_25k.CNV-profile.bedGraph

As @PinpinSui said, with a higher binsize (50kb in my case) it worked.