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  3. Chicago

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Issues (26–50 of 82)

Title T P Status Votes Assignee Created Updated Actions
#26: all interactions filtered out - error
bug major new
chicagoTeam
#27: Not able to generate .baitmap files using create_baitmap_rmap.pl
task minor resolved
#28: BAM2chicago awk error
bug major resolved
#29: Bam2chicago: no such file or directory
bug major resolved
#30: makeDesignFiles.py
bug major resolved
#31: advice for assessing concordance between primary capture and reciprocal capture results
task major resolved
#32: Chicago package cannot using its own truncated maxLBrownEst
bug major new
#33: bam2chicago.sh worng number of fields
bug 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
#35: Cut2 odd behaviour
bug major new
#36: Can I change the threshold?
task major resolved
#37: makeDesignFiles.py compatible with python3
proposal major new
#38: Chicago pipeline for R studio?
proposal critical resolved
#39: after hicup, rmap baitmap and runchicago.r
enhancement major new
#40: problems with calibration
task major new
#41: bam2chicago problem
bug major 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
#43: 'bam2chicago.sh' problem
bug major new
#44: WashU output
bug major new
#45: Can't change --removeb2b value when I'm doing the design file
bug major new
#46: About bam2chicago.sh error
bug major new
#47: runChicago.R errors during "Reading NBaitsPerBin file" step
bug major new 1
#48: Chicago works with each two of three replicates, but not with all three together
bug major resolved
#49: Assign designDir path to a Chicago object
task major new
#50: makeDesignFiles.py: ValueError: invalid literal for int() with base 10: 'start'
bug major resolved
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