Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / dpryan79/MethylDackel issues and pull requests
#148 - Could not repeat a CpG extraction with the same reference file and its index
Issue -
State: open - Opened by sttongjai about 1 year ago
#147 - about M-bias
Issue -
State: closed - Opened by feihongloveworld over 1 year ago
- 1 comment
#146 - Positions in cytosine_report did not match the regions in providing bed file
Issue -
State: open - Opened by huichanghuang over 1 year ago
#145 - Does indel effect the methylation calling or C context determination
Issue -
State: open - Opened by huichanghuang over 1 year ago
- 1 comment
#144 - Fix end trimming off-by-one that caused overflow into qual and seq
Pull Request -
State: closed - Opened by limwz01 over 1 year ago
- 2 comments
#143 - Fix wrong mapping position used for overlap computation
Pull Request -
State: closed - Opened by limwz01 over 1 year ago
- 1 comment
#142 - mbias
Issue -
State: open - Opened by jsikora93 over 1 year ago
- 1 comment
#141 - Coverage of C sites
Issue -
State: closed - Opened by jsikora93 over 1 year ago
- 1 comment
#140 - Clarification on definition of "unmethylated C"
Issue -
State: closed - Opened by cvenney over 1 year ago
- 1 comment
#139 - Installation failure: "bigWig.h: No such file or directory"
Issue -
State: open - Opened by phongphak almost 2 years ago
- 1 comment
#138 - CURL_OPENSSL conflict with samtools
Issue -
State: open - Opened by shraddhapai almost 2 years ago
- 3 comments
#137 - mbias result is different between bismark and bwameth output
Issue -
State: closed - Opened by nnlrl about 2 years ago
- 1 comment
#136 - per-fragment methylation
Issue -
State: open - Opened by BeyondTheProof about 2 years ago
- 1 comment
#135 - Genome browsing from MethylDackel bedGraphCpG file
Issue -
State: open - Opened by emiliomastriani over 2 years ago
#134 - Understanding --minConversionEfficiency argument
Issue -
State: closed - Opened by TSolDour over 2 years ago
- 1 comment
#133 - Stand output
Issue -
State: open - Opened by simonbrd over 2 years ago
- 1 comment
#132 - Chromosomes effected by methylation
Issue -
State: closed - Opened by emiliomastriani over 2 years ago
- 4 comments
#131 - Methylation profile for large genome organisms
Issue -
State: open - Opened by awieeeee over 2 years ago
- 5 comments
#130 - do not recompile on "make test" and "make install"
Pull Request -
State: closed - Opened by zemu-unile over 2 years ago
#129 - perRead output - print Bismark methylation call string?
Issue -
State: open - Opened by embertucci almost 3 years ago
- 3 comments
#128 - why cytosine_report output blank file?
Issue -
State: open - Opened by realzhang almost 3 years ago
#127 - Strand specific extraction
Issue -
State: closed - Opened by Tschichen almost 3 years ago
- 2 comments
#126 - Corrects invalid link
Pull Request -
State: closed - Opened by bwlang almost 3 years ago
#125 - implement #122, the --ignoreNH option
Pull Request -
State: closed - Opened by dpryan79 about 3 years ago
- 1 comment
#124 - adds mappability to readme
Pull Request -
State: closed - Opened by bwlang about 3 years ago
#123 - maxVariantFrac
Issue -
State: open - Opened by Dingersrun about 3 years ago
- 3 comments
#122 - Min mapq option seems to be ignored / -q setting has no effect
Issue -
State: closed - Opened by DaGaMs about 3 years ago
- 8 comments
#121 - cytosine report and minConversionEfficiency
Issue -
State: closed - Opened by nchernia about 3 years ago
- 1 comment
#120 - Fixed segfault with mappability filtering, minor fixes.
Pull Request -
State: closed - Opened by Valiec about 3 years ago
- 2 comments
#119 - Implement #61, allow filtering by non-CpG conversion efficiency. Also…
Pull Request -
State: closed - Opened by dpryan79 about 3 years ago
#118 - Fix #117, bump version to 0.5.3
Pull Request -
State: closed - Opened by dpryan79 over 3 years ago
- 1 comment
#117 - perRead --requireFlags and --ignoreFlags not working properly
Issue -
State: closed - Opened by abcoxyzide over 3 years ago
- 1 comment
#116 - cytosine_report differences and question
Issue -
State: open - Opened by nchernia over 3 years ago
- 3 comments
#115 - perRead Invalid option '?'
Issue -
State: closed - Opened by nchernia over 3 years ago
- 3 comments
#114 - the -p option about a overlapping read
Issue -
State: closed - Opened by gill0110 over 3 years ago
- 1 comment
#113 - Reimplement pileup overlap detection
Pull Request -
State: closed - Opened by dpryan79 over 3 years ago
- 1 comment
#112 - --OT and --OB suggestions by mbias produce "Invalid bounds string"
Issue -
State: open - Opened by DaGaMs over 3 years ago
- 7 comments
#111 - Regarding #109
Pull Request -
State: open - Opened by vivekbhr over 3 years ago
#110 - Can MethylDackel run for pbat?
Issue -
State: open - Opened by ifishlin over 3 years ago
- 4 comments
#109 - methyldackel for GCH context
Issue -
State: open - Opened by vivekbhr over 3 years ago
- 1 comment
#108 - nOT, nOB argument for tagmentation-based WGBS
Issue -
State: closed - Opened by ifishlin over 3 years ago
- 1 comment
#107 - Incorrect strand assignment for single-end, non-directional libraries from Bismark
Issue -
State: open - Opened by mattsoup over 3 years ago
- 2 comments
#106 - Compilation error - linker error
Issue -
State: open - Opened by mpBioinf almost 4 years ago
- 3 comments
#105 - Segmentation fault with extract command
Issue -
State: closed - Opened by nilaycan almost 4 years ago
- 1 comment
#104 - Counts reported for G positions
Issue -
State: closed - Opened by dataMaster-Kris almost 4 years ago
- 1 comment
#103 - methylDackel extract segmentation fault
Issue -
State: open - Opened by acontrerasg about 4 years ago
- 1 comment
#102 - How to exclude the first 10bp of each read, irrespective of orientation
Issue -
State: open - Opened by DaGaMs over 4 years ago
- 9 comments
#101 - "Invalid bounds string" with the example setting from the help
Issue -
State: open - Opened by DaGaMs over 4 years ago
- 6 comments
#100 - The extraction speed differs a lot between bams from different mapping software
Issue -
State: closed - Opened by chenzixi07 over 4 years ago
- 4 comments
#99 - MethylDackel core dump Ubintu 18.04 (problem happend again in issue #95)
Issue -
State: closed - Opened by tahuh over 4 years ago
- 30 comments
#98 - Methylation percentage calculation
Issue -
State: open - Opened by jrice128 over 4 years ago
- 1 comment
#97 - Usage in Other Experiments?
Issue -
State: closed - Opened by YogiOnBioinformatics over 4 years ago
- 1 comment
#96 - Fix issue 93
Pull Request -
State: closed - Opened by dpryan79 over 4 years ago
#95 - MethylDacke extract core dump un Ubuntu 18.04
Issue -
State: closed - Opened by tahuh over 4 years ago
- 1 comment
#94 - Instruction on only trimming reads that are below a certain insert length
Issue -
State: open - Opened by ptgriff over 4 years ago
- 5 comments
#93 - MethylDackel mbias: Segmentation fault (core dumped) on CentOS 8.0
Issue -
State: closed - Opened by luuloi over 4 years ago
- 10 comments
#92 - Coverage plot
Issue -
State: closed - Opened by demis001 over 4 years ago
- 5 comments
#91 - Fix issue 88
Pull Request -
State: closed - Opened by dpryan79 over 4 years ago
#90 - default extract flags incompatible with RRBS
Issue -
State: closed - Opened by rmvpaeme over 4 years ago
- 2 comments
#89 - Fixing typo
Pull Request -
State: closed - Opened by wdecoster over 4 years ago
- 1 comment
#88 - Chromosome label inconsistencies in --cytosine_report
Issue -
State: closed - Opened by jeffbhasin almost 5 years ago
- 2 comments
#87 - see if this fixes the CI
Pull Request -
State: closed - Opened by dpryan79 almost 5 years ago
#86 - GpC Methylation
Issue -
State: open - Opened by allison4 about 5 years ago
- 6 comments
#85 - License undeclared
Issue -
State: closed - Opened by rekado about 5 years ago
- 2 comments
#84 - Excluding bases from the methylation bias plot
Issue -
State: closed - Opened by ToPrinz about 5 years ago
- 8 comments
#83 - mbias segmentaion fault
Issue -
State: closed - Opened by vanessayang0927 about 5 years ago
- 2 comments
#82 - MethylDackel won't compile
Issue -
State: closed - Opened by mblanche about 5 years ago
- 9 comments
#81 - Destranding?
Issue -
State: open - Opened by ToPrinz about 5 years ago
- 2 comments
#80 - [WIP] Adding the ability to filter reads by Bismap mappability
Pull Request -
State: closed - Opened by Valiec over 5 years ago
- 1 comment
#79 - mbias --keepDupes and -F argument parsing
Issue -
State: open - Opened by bwlang over 5 years ago
#78 - methylation calls from spliced alignments
Issue -
State: closed - Opened by al2na over 5 years ago
- 2 comments
#77 - Fix #58
Pull Request -
State: closed - Opened by dpryan79 over 5 years ago
#76 - No CI outside of [0, 1]
Pull Request -
State: closed - Opened by dpryan79 over 5 years ago
#75 - External htslib
Pull Request -
State: closed - Opened by dpryan79 over 5 years ago
#74 - per-read and per-CpG metrics for bs-seeker2
Issue -
State: closed - Opened by retrogenomics over 5 years ago
- 3 comments
#73 - threading related miscounting in mbias
Issue -
State: closed - Opened by bwlang over 5 years ago
- 4 comments
#72 - added limits.h to resolve MAX_INT on osx
Pull Request -
State: closed - Opened by hillst over 5 years ago
- 1 comment
#71 - External htslib
Pull Request -
State: closed - Opened by dpryan79 over 5 years ago
#70 - Per read metrics
Pull Request -
State: closed - Opened by dpryan79 over 5 years ago
#69 - allow to specify bai manually
Issue -
State: closed - Opened by antonkulaga over 5 years ago
- 1 comment
#68 - save the output to working folder or let the user configure the output folder
Issue -
State: closed - Opened by antonkulaga over 5 years ago
- 1 comment
#67 - what is format of the inputfile ?
Issue -
State: closed - Opened by hmyh1202 over 5 years ago
- 2 comments
#66 - About the sam flag for methylation extract
Issue -
State: closed - Opened by chhylp123 almost 6 years ago
- 3 comments
#65 - error: [fai_fetch_seq] The sequence "chr1_CT_converted" not found
Issue -
State: closed - Opened by Faten-Taki about 6 years ago
- 8 comments
#64 - Segfault occasionally in MethylDackel mbias
Issue -
State: closed - Opened by bwlang about 6 years ago
- 2 comments
#63 - methylKit-compatible output
Issue -
State: closed - Opened by MoutonAlice about 6 years ago
- 1 comment
#62 - dot in the 4th column of
Issue -
State: closed - Opened by yij047 about 6 years ago
- 6 comments
#61 - remove/exclude reads with densely un-converted non-CpG sites
Issue -
State: closed - Opened by avilella over 6 years ago
- 3 comments
#60 - Min Depth of Coverage
Issue -
State: closed - Opened by agustinmora over 6 years ago
- 2 comments
#59 - Confidence intervals shouldn't b <0 or > 1
Issue -
State: closed - Opened by dpryan79 over 6 years ago
#58 - --keepDupes and -F 0x400 gives me different results
Issue -
State: closed - Opened by crazyhottommy over 6 years ago
- 8 comments
Labels: bug
#57 - methylKit
Issue -
State: closed - Opened by nchernia over 6 years ago
- 1 comment
#56 - Methylation per read
Issue -
State: closed - Opened by nchernia over 6 years ago
- 24 comments
#55 - log with different loses
Issue -
State: open - Opened by avilella over 6 years ago
- 4 comments
#54 - Specific non CpG context
Issue -
State: closed - Opened by ghost almost 7 years ago
- 1 comment
#53 - empty output
Issue -
State: closed - Opened by antoine4ucsd almost 7 years ago
- 6 comments
#52 - paired-end mode calling
Issue -
State: open - Opened by avilella about 7 years ago
- 2 comments
#51 - Implement --cytosine_report
Pull Request -
State: closed - Opened by dpryan79 about 7 years ago
#50 - discrepancy between MethylDackel and IGV PBAT-style data aligned with bwameth
Issue -
State: open - Opened by avilella about 7 years ago
- 11 comments
#49 - Updates README.md with which strand contains information
Pull Request -
State: closed - Opened by bwlang about 7 years ago
- 4 comments