FitHiChIP is a computational method for identifying chromatin contacts among regulatory regions such as enhancers and promoters from HiChIP/PLAC-seq data. FitHiChIP jointly models the non-uniform coverage and genomic distance scaling of HiChIP data, captures previously validated enhancer interactions for several genes including MYC and TP53, and recovers contacts genome-wide that are supported by ChIA-PET, promoter capture Hi-C and Hi-C data.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --mem=8g -c10 --gres=lscratch:20 [user@cn3316 ~]$ module load FitHiChIP [+] Loading singularity/3.10.5 on cn3316 [+] Loading FitHiChIP 11.0 [user@cn3316 ~]$ mkdir -p /data/$USER/FitHiChIP && cd /data/$USER/FitHiChIPCopy the source code folder and the sample sample data folder to your current directory:
[user@cn3316 ~]$ cp -r $FITHICHIP_SRC/* . [user@cn3316 ~]$ cp -r $FITHICHIP_DATA .Run the FitHiChIP_HiCPro.sh executable in the source folder:
[user@cn3316 ~]$ ./FitHiChIP_HiCPro.sh -C configfile_test ================ Parsing input configuration file ================= ... ================ Verifying input configuration parameters ================= ... ====== Changing relative pathnames of the input files to their absolute path names ========== ... ====== Final checing of input parameters ========== ====== Writing input parameters ========== ... ================ Processing HiC-pro generated valid pairs and / or matrix files provided as input ================= ====>> Computing HiC-pro matrices from the input valid pairs file ====>> Executable to generate contact matrix from valid pairs: /usr/local/apps/FitHiChIP/11.0/bin/build_matrix ***** HiC-pro input valid pairs file in gzipped format ====>> Created file : /data/user/FitHiChIP/TestData/results/Matrix_BinSize5000/Matrix_abs.bed ====>> Created file : /data/user/FitHiChIP/TestData/results/Matrix_BinSize5000/Matrix.matrix ================ Creating input interactions (bin pairs + CC) ================= ... ======= Generated interaction file : /data/user/FitHiChIP/TestData/results/Matrix_BinSize5000/FitHiChIP.interactions.initial.bed ==>>> Number of locus pairs with nonzero contact count (without any distance thresholding): 2364391 ======= Limiting input interactions to the specified distance ranges 5000 to 1000000 ========= ... ===>> Number of cis pairs with nonzero contact count (after distance thresholding): 726467 ================ Generating coverage statistics and bias for individual bins ================= ... Computing 1D coverage - Processing chromosome : chr1 -- number of input peaks for this chromosome : 4175 Computing 1D coverage - Processing chromosome : chr10 -- number of input peaks for this chromosome : 1797 Computing 1D coverage - Processing chromosome : chr11 -- number of input peaks for this chromosome : 2155 ... Computing 1D coverage - Processing chromosome : chrX -- number of input peaks for this chromosome : 1161 Computing 1D coverage - Processing chromosome : chrY -- number of input peaks for this chromosome : 156 ... ================ Computing bias statistics - coverage bias will be employed ================= R... ================ creating full feature file for FitHiChIP ================= ======== Created full feature file : /data/user/FitHiChIP/TestData/results/NormFeatures/Coverage_Bias/FitHiChIP.AllBin_CompleteFeat.bed ================ Generating interactions + features for significance estimation ================= ... **** Start of while Loop ----- current interaction type: 3 ****** ============ Calling significant interactions =============== ... ===>> Total Number of input interactions (locus pairs): 312536 ****** Total number of training interactions: 312536 ******** ****** Number of contacts per bin (allowed for equal occupancy binning): 2746 ******** ... ==>>> modeled the bias regression -- time: 0.646705150604248 *** NumElem: 312536 ExpTotContact : 432569 *** Modeling regression bias probability based P value --- uniq distance idx: 1 si: 1 ei: 26635 num elem : 26635 *** Modeling regression bias probability based P value --- uniq distance idx: 2 si: 26636 ei: 45246 num elem : 18611 *** Modeling regression bias probability based P value --- uniq distance idx: 3 si: 45247 ei: 59613 num elem : 14367 ... *** Modeling regression bias probability based P value --- uniq distance idx: 198 si: 311681 ei: 311962 num elem : 282 *** Modeling regression bias probability based P value --- uniq distance idx: 199 si: 311963 ei: 312238 num elem : 276 *** Modeling regression bias probability based P value --- uniq distance idx: 200 si: 312239 ei: 312536 num elem : 298 *** p-value estimation is complete for the bias regression **** ******** FINISHED calling significant interactions ----- Extracted significant interactions ---- FDR threshold lower than: 0.01 ... ********** Merged filtering option is true ************ ******** applying merge filtering on the FitHiChIP significant interactions ****** ****** Merge filtering of adjacent loops is enabled ***** ***** within function of merged filtering - printing the parameters *** *** bin_size: 5000 *** headerInp: 1 *** connectivity_rule: 8 *** TopPctElem: 100 *** NeighborHoodBinThr: 10000 *** QValCol: 26 *** PValCol: 25 *** SortOrder: 0 ==================== End of merge filtering adjacent interactions !!! ====================== ----- Applied merged filtering (connected component model) on the adjacent loops of FitHiChIP pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (1882 records, 18 fields): 13 millis /bin/bash: /opt/conda/envs/fithichip/lib/libtinfo.so.6: no version information available (required by /bin/bash) ---- Within function of plotting distance vs contact count ---- Input interaction file: /data/user/FitHiChIP/TestData/results/FitHiChIP_Peak2ALL_b5000_L5000_U1000000/P2PBckgr_0/Coverage_Bias/FitHiC_BiasCorr/Merge_Nearby_Interactions/FitHiChIP.interactions_FitHiC_Q0.01_MergeNearContacts.bed Output plot file: /data/user/FitHiChIP/TestData/results/FitHiChIP_Peak2ALL_b5000_L5000_U1000000/P2PBckgr_0/Coverage_Bias/FitHiC_BiasCorr/Merge_Nearby_Interactions/FitHiChIP.interactions_FitHiC_Q0.01_MergeNearContacts_Dist_CC.png Warning message: Removed 1 rows containing missing values (`geom_bar()`). Merged filtering significant interactions - created various epigenome browser compatible files for these interactions!!! Updated CurrIntType: 4 **** Now summarizing FitHiChIP results in the HTML file *** ***** FitHiChIP pipeline is completely executed - congratulations !!! *****Likewise, FitHiChIP can be run with other configuration files.
[user@cn3316 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. fithichip.sh). For example:
#!/bin/bash module load FitHiChIP FitHiChIP_HiCPro.sh -C configfile_1 FitHiChIP_HiCPro.sh -C configfile_2 FitHiChIP_HiCPro.sh -C configfile_3 FitHiChIP_HiCPro.sh -C configfile_4
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] fithichip.sh