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  3. Chicago

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Issues (1–25 of 26)

Title T P Status Votes Assignee Created Updated Actions
#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
#25: Reads filtered from chinput file?
bug major resolved
chicagoTeam
#29: Bam2chicago: no such file or directory
bug major resolved
#28: BAM2chicago awk error
bug major resolved
#21: Error while running readAndMerge()
bug major resolved
chicagoTeam
#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
#10: Differing numbers of interactions reported in seqmonk and washU output files
bug major resolved
chicagoTeam
#12: correct workflow for weight recalibration
task major resolved
chicagoTeam
#7: ./bam2chicago.sh errors
bug major resolved
chicagoTeam
#8: Error in normaliseOtherEnds when combining multiple datsets
bug major resolved
chicagoTeam
#3: Different problems running replicates
bug major resolved
chicagoTeam
#4: .chinput does not show actual distance?
bug major resolved
chicagoTeam
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