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  3. Chicago

Issues

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Issues (26–50 of 65)

Title T P Status Votes Assignee Created Updated Actions
#45: Can't change --removeb2b value when I'm doing the design file
bug major new
#44: WashU output
bug major new
#40: problems with calibration
task major new
#41: bam2chicago problem
bug major new
#39: after hicup, rmap baitmap and runchicago.r
enhancement major new
#37: makeDesignFiles.py compatible with python3
proposal major new
#35: Cut2 odd behaviour
bug major new
#33: bam2chicago.sh worng number of fields
bug major new
#32: Chicago package cannot using its own truncated maxLBrownEst
bug major new
#26: all interactions filtered out - error
bug major new
chicagoTeam
#22: run Chicago Error
bug major new
#23: Is it possible to set a random seed - each run of chicago yields a different number of interactions
proposal major new
chicagoTeam
#19: runChicago Error
bug major new
#70: runChicago.R error
bug major open
#15: Input files and how to get them
task major resolved
#63: Unable to replicate results from chicagoPipeline()
enhancement major resolved 1
#52: 4 Cutter Capture HiC
enhancement major resolved
#51: --en-feat-list
bug major resolved
#48: Chicago works with each two of three replicates, but not with all three together
bug major resolved
#50: makeDesignFiles.py: ValueError: invalid literal for int() with base 10: 'start'
bug major resolved
#36: Can I change the threshold?
task major resolved
#31: advice for assessing concordance between primary capture and reciprocal capture results
task major resolved
#30: makeDesignFiles.py
bug major resolved
#24: Intersecting interactions from replicates
task major resolved
chicagoTeam
#17: runChicago.R
task major resolved
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