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IDR
Hi, Can someone please help me understand this error. I have installed the latest version and using two replicate peak files. Thanks
Hi, I am using idr to process 2 replicate bed files but getting an index error. copying command and bash response idr --samples dyadvscolrep1_c3.0_common.bed dyadvscolrep2_c3.0_common.bed /usr/local/bin/idr --samples dyadvscolrep1_c3.0_common.bed dyadvscolrep2_c3.0_common.bed Traceback...
Hello! After I install the idr-2.0.2 and run idr --samples tests/data/peak1 tests/data/peak2, the error comes: ValueError: The truth value of an array with more than one element is ambiguous. Use...
Hi, I am working on Chip-seq data for evaluating the consistency between replicate using idr. I had some questions about ${POOLED_PEAK_FILE}. Where can we find the information to generate the...
Hi, I want to use IDR to get highly repetitive peaks. For each biological repetition, we called peaks separately using SICER to get broad peaks. The output file of the...
I installed lastest IDR (2.0.3) with: `python3 setup.py install --/mnt/data0/lizhidan/software/idr-2.0.3` then, ran: `idr` got: ` File "/home/lizhidan/.local/bin/idr", line 4, in __import__('pkg_resources').run_script('idr==2.0.3', 'idr') File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 3254, in def _initialize_master_working_set(): File...
Hi, I am just running the manual code: idr --samples peak1 peak2 and this is the output: Initial parameter values: [0.10 1.00 0.20 0.50] Final parameter values: [1.57 1.26 0.89...
Dear IDR developers, Could you please help me with this issue. IDR pipeline gives me these pictures and I see that highly reproducible top peaks have high IDR p values....
Hi, I am trying to run IDR on a set of 3 replicates and I get the following error: idr: error: unrecognized arguments: K9AcY4_2/MACS2_K9acY4_2/K9acY4_2_macs2_peaks.broadPeak This is the third replicate. If...
Hi! I want to use IDR on peaks file obtained using HMMRATAC pipeline. From this pipeline, we obtained a list of peaks in gappedPeak format (score in the 13th column)...
