Closed LHXqwq closed 3 days ago
Do you only have 2 input marks? The default initialization mode can only handle 2^(number of input mark) states but you are asking for 10 states
Yes, I currently only have data for H3K4me3 and H3K27ac. Can ChromHMM be used to roughly identify enhancers and promoters based solely on these two datasets?
Yes. You would need to either use at most 4 states or if using more than 4 states use the '-init random' flag
When I run java -mx1600M -jar ChromHMM.jar LearnModel -b 200 Input_FC2 Output_FC2_4 4 ss11, the following error occurs:
Writing to file Output_FC2_4_2/ss11_4_segments.bed Writing to file Output_FC2_4_2/ss11_4_dense.bed Writing to file Output_FC2_4_2/ss11_4_expanded.bed Writing to file Output_FC2_4_2/ss11_4_overlap.txt Writing to file Output_FC2_4_2/ss11_4_overlap.png Writing to file Output_FC2_4_2/ss11_4_overlap.svg Exception in thread "main" java.lang.NumberFormatException: For input string: "-" at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.base/java.lang.Integer.parseInt(Integer.java:642) at java.base/java.lang.Integer.parseInt(Integer.java:770) at edu.mit.compbio.ChromHMM.StateAnalysis.neighborhoodMax(StateAnalysis.java:2942) at edu.mit.compbio.ChromHMM.ChromHMM.main(ChromHMM.java:15459)
What could be the cause? I did not find the '-' character in the files under the Input_FC2 folder.
I think there is a '-' in a file in the ss11 folder of ANCHORFILES. Did you check there?
Thank you very much. The issue was with a file in the ss11 folder of ANCHORFILES where there was a space in the second column. I have now successfully run the process and obtained the corresponding results.
The contents of emissions_4.txt are as follows:: State (Emission order) H3K27ac H3K4me3 1 0.7371722491995913 0.025454951706880308 2 0.0070734777583484985 2.808219552645712E-4 3 0.9531553476199173 0.9489478579210275 4 0.0526273184047077 0.8673363187489265
In the ss11_4_expanded.bed file, I noticed the following correspondence between state and color: State color 1 0,0,255 2 0,102,0 3 51,255,153 4 255,255,0
Could you please tell me which of the 15 states these 4 states correspond to? For example (Active Promoter, Weak Promoter, Strong Enhancer, Weak/Poised Enhancer, etc.).
Have you run enrichments for annotated TSS/promoter regions?
Yes, the content of ss11_4_overlap.txt is as follows:
State (Emission order) Genome % RefSeqExon.ss11.bed.gz RefSeqGene.ss11.bed.gz RefSeqTES.ss11.bed.gz RefSeqTSS.ss11.bed.gz RefSeqTSS2kb.ss11.bed.gz 1 2.03495 5.15444 2.27030 3.58753 22.34702 15.81526 2 90.84071 0.81031 0.90967 0.85598 0.37223 0.45504 3 1.71311 3.78950 1.71852 3.00031 10.22387 12.69401 4 5.41123 1.73893 1.81115 1.81144 0.59076 0.87486 Base 100 0.3060868984 5.6918859806 0.0001805545 0.0001824023 0.7014005474
I am working on enhancer identification for the first time and am not quite sure how this information can help identify enhancers.
I find it odd that you are not seeing TSS enrichment in state 4 associated with H3K4me3. You might want to double check the emission parameters correspond to the final version of the model the enrichments are based on and/or your H3K4me3 data is ok.
When I run the following command:
java -mx1600M -jar ChromHMM.jar LearnModel -b 200 Input_FC2 Output_FC2_10 10 hg19
I encountered the following error. What could be the potential issue?
Exception in thread "main" java.lang.IllegalArgumentException: On this data the INFORMATION initialization strategy can only support 4 states. Check if the binarization was done correctly, and if so use the RANDOM or LOAD options for more states at edu.mit.compbio.ChromHMM.ChromHMM.informationInitializeNested(ChromHMM.java:2675) at edu.mit.compbio.ChromHMM.ChromHMM.buildModel(ChromHMM.java:1036) at edu.mit.compbio.ChromHMM.ChromHMM.main(ChromHMM.java:15223)