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Issues list

Multiple sites failed to process during dmr pair build-available custom build produced for fix.
#149 by ArnavBharti was closed Apr 16, 2024
11
Issue when inserting a region BED file build-available custom build produced for fix.
#146 by lance0499 was closed Apr 16, 2024
6
Is there a way to have modkit handle duplicate reads? build-available custom build produced for fix.
#145 by billytcl was closed Apr 16, 2024
4
Modkit dmr pair not taking in multiple replicates
#142 by lance0499 was closed Mar 7, 2024
3
[docs] Documentation on GH Pages down
#141 by ArtRand was closed Mar 5, 2024
1
Using multiple samples in modkit dmr build-available custom build produced for fix.
#140 by ArnavBharti was closed Mar 17, 2024
12
Convert bam to pseudo bisulfite output build-available custom build produced for fix.
#139 by faulk-lab was closed Jun 24, 2024
38
pyspoa
#138 by kawito was closed Feb 26, 2024
3
bedmethyl Nvalid coverage vs samtools depth coverage
#137 by osvatic was closed Feb 22, 2024
2
Missing --allow-non-primary Option in Extract Command Documentation and Execution Error
#136 by gilaovadia1 was closed Mar 5, 2024
2
failed to run custom build command for `openssl-sys v0.9.99
#130 by vetmohit89 was closed Feb 16, 2024
2
% in modkit pileup Vs modkit extract
#129 by Macdot3 was closed Feb 16, 2024
9
Valid coverage with DRACH motif pileup modkit pileup question Looking for clarification on inputs and/or outputs
#127 by mbosm was closed Feb 16, 2024
3
modkit repair - update MN tags? build-available custom build produced for fix. repair modkit repair
#126 by jkh00 was closed Mar 5, 2024
4
Pull different methylation types from different bam files
#124 by Ge0rges was closed Feb 5, 2024
3
p values for DMR scores? DMR modkit dmr question Looking for clarification on inputs and/or outputs
#122 by EpiAllele was closed Mar 5, 2024
6
Modkit Extract Kmer Size Limit build-available custom build produced for fix. extract modkit extract
#121 by andrewgalbraith21 was closed Mar 5, 2024
9
MM and ML tags are not present in mapped SAM
#120 by hamid89 was closed Jan 26, 2024
Extract 5mCG/5hmCG modification from 5mC_5hmC BAM file. enhancement New feature or request extract modkit extract
#118 by miwi610 was closed Jan 26, 2024
3
Plans to make modkit able to output MetH5 format files?
#117 by bernardo-heberle was closed Jan 19, 2024
2
Ignore soft-clippings in pileup question Looking for clarification on inputs and/or outputs
#115 by SophieValk was closed Jan 22, 2024
3
Difference Ncanonical and Ndiff (IGV settings) question Looking for clarification on inputs and/or outputs
#114 by SophieValk was closed Jan 22, 2024
5
Missing data chrM bedMethyl file
#112 by Macdot3 was closed Jan 16, 2024
1
Thanks, Arthur! Just noticed that --include-positions pileups CpG sites a base level in a provided region. Does modkit have a function that pileups and accumulates all CpG sites within a region? Something like the "dmr" function but without comparisons between samples. Thx!
#111 by kwglam was closed Jan 11, 2024
modkit pileup --region error
#110 by kwglam was closed Jan 11, 2024
4
ProTip! Updated in the last three days: updated:>2024-08-03.