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  3. Chicago

Issues

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Issues (1–25 of 82)

Title T P Status Votes Assignee Created Updated Actions
#15: Input files and how to get them
task major resolved
#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
#36: Can I change the threshold?
task major resolved
#31: advice for assessing concordance between primary capture and reciprocal capture results
task major resolved
#24: Intersecting interactions from replicates
task major resolved
chicagoTeam
#17: runChicago.R
task major resolved
#27: Not able to generate .baitmap files using create_baitmap_rmap.pl
task minor resolved
#18: en_full_cis_range and en-trans
task major resolved
#14: bam2chicago bedtools error
task major resolved
#13: Minimum spacing between viewpoints?
task major resolved
chicagoTeam
#11: Altering rmap files in specific genomic regions
task major resolved
#12: correct workflow for weight recalibration
task major resolved
chicagoTeam
#68: parameters setting for double cutters GATC (DpnII) and GANTC
proposal major new 3
#38: Chicago pipeline for R studio?
proposal critical resolved
#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
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