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  3. Chicago

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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
#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
#79: ERROR :: Oligos file, rmap and baitmap production (DpnII enzyme HICUP)
bug critical closed
#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
#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
#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
#71: Question about output options in runChicago.R
enhancement major new
#70: runChicago.R error
bug major open
#69: Issue with bam2chicago.sh
bug major new
#54: What does the following messenge mean after I ran runChicago.R
bug critical new
#43: 'bam2chicago.sh' problem
bug major new
#66: Bait Coordinates don't intersect with .rmap file
bug major new
#61: install Chicago Error: Failed to install 'unknown package' from Bitbucket:
bug major new
#65: Error during runChicago.R
bug major new
#64: runChicago.R: The Brownian OE factors look weird
bug minor new
#60: Error in if (cj == upper) next : missing value where TRUE/FALSE needed Calls: chicagoPipeline -> normaliseOtherEnds -> .addTLB -> cut2
bug major new
#62: OLwithSI in peakEnrichment4Features
bug minor new
#56: bam2chicago.sh error: empty baitOnRight.bedpe file
bug major new
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