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  3. Chicago

Issues

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Issues (1–25 of 48)

Title T P Status Votes Assignee Created Updated Actions
#73: issue with running makeDesignFiles_py3.py
task major new
#74: baitmap file
task minor new
#72: Can I run CHiCAGO with captureC data?
task minor new
#57: Using juicer .hic for creating input files for Chicago
task critical new
#49: Assign designDir path to a Chicago object
task major new
#40: problems with calibration
task major new
#68: parameters setting for double cutters GATC (DpnII) and GANTC
proposal major new 3
#37: makeDesignFiles.py compatible with python3
proposal major new
#34: why there is significant difference in chicago output , when valid pairs are used from HiC Pro and HiCUP and which one is reliable ? and why chicago output also gives trans interaction as significant ?
proposal minor new
#23: Is it possible to set a random seed - each run of chicago yields a different number of interactions
proposal major new
chicagoTeam
#9: Examples data / playground data
proposal minor new
#42: create_baitmap_rmap.pl: error:Could not find '1 310' in digest_fragments hash - the digest file and oligo probes file appear to be incompatible.
enhancement major new
#71: Question about output options in runChicago.R
enhancement major new
#53: Small capture library
enhancement major new
#39: after hicup, rmap baitmap and runchicago.r
enhancement major new
#82: Where can Oligos file get?
bug major new
#81: How to get gene-wise score?
bug major new
#78: Error: between has been passed an argument x of type logical
bug major new
#80: How to creat my .baitmap file?
bug major new
#47: runChicago.R errors during "Reading NBaitsPerBin file" step
bug major new 1
#77: bam2chicago.sh breaking in the "Flipping all reads that overlap with the bait on to the right-hand side..."
bug major new
#76: makeBins.R generates spurious bait fragments
bug major new
#75: potential bug in estimateTechnicalNoise
bug major new
#69: Issue with bam2chicago.sh
bug major new
#54: What does the following messenge mean after I ran runChicago.R
bug critical new
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