Ecosyste.ms: Issues

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GitHub / dpryan79/MethylDackel issues and pull requests

#147 - about M-bias

Issue - State: closed - Opened by feihongloveworld over 1 year ago - 1 comment

#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

#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

#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