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Issues list

DMR pair analysis - output .bed clarification
#223 by physnano was closed Jul 3, 2024 updated Jul 3, 2024
1
Turning off --cpg Modkit argument via wf-human-variation question Looking for clarification on inputs and/or outputs
#221 by hassebossenbroek was closed Jul 2, 2024 updated Jul 2, 2024
3
dmr multi failed to load samples build-available custom build produced for fix. troubleshooting workflow and data preparation questions
#207 by nickst85 was closed Jun 26, 2024 updated Jun 26, 2024
6
find-motifs fails to load before_file question Looking for clarification on inputs and/or outputs
#218 by Ge0rges was closed Jun 24, 2024 updated Jun 24, 2024
2
Convert bam to pseudo bisulfite output build-available custom build produced for fix.
#139 by faulk-lab was closed Jun 24, 2024 updated Jun 24, 2024
38
pseudouridylation extracting question Looking for clarification on inputs and/or outputs
#193 by Papareddy was closed Jun 24, 2024 updated Jun 24, 2024
3
error: unrecognized subcommand 'find-motifs' (Find highly modified motif sequences) question Looking for clarification on inputs and/or outputs
#187 by saky7009 was closed Jun 24, 2024 updated Jun 24, 2024
3
extract options question Looking for clarification on inputs and/or outputs
#215 by Baix7 was closed Jun 24, 2024 updated Jun 24, 2024
4
modkit call-mods omits all modification information for many RNA004 reads bug Something isn't working build-available custom build produced for fix.
#202 by pre-mRNA was closed Jun 24, 2024 updated Jun 24, 2024
5
Getting error when running modkit dmr pair bug Something isn't working build-available custom build produced for fix.
#208 by agoel13 was closed Jun 24, 2024 updated Jun 24, 2024
5
Contig names source question Looking for clarification on inputs and/or outputs
#213 by Ge0rges was closed Jun 19, 2024 updated Jun 19, 2024
2
How to generate hydroxymethylation in pileup? question Looking for clarification on inputs and/or outputs
#206 by weishwu was closed Jun 18, 2024 updated Jun 19, 2024
9
Bug in find_motifs bug Something isn't working
#203 by Ge0rges was closed Jun 13, 2024 updated Jun 13, 2024
6
pileup output both bedMethyl and bedGraph
#204 by Ge0rges was closed Jun 11, 2024 updated Jun 11, 2024
2
API for modkit extract read_calls_path output? build-available custom build produced for fix. enhancement New feature or request
#194 by billytcl was closed Jun 11, 2024 updated Jun 11, 2024
8
Question about dmr score question Looking for clarification on inputs and/or outputs
#93 by Ge0rges was closed Mar 5, 2024 updated Jun 10, 2024
13
CpG Calling with Reference question Looking for clarification on inputs and/or outputs
#196 by SophieValk was closed Jun 10, 2024 updated Jun 10, 2024
2
Does pileup always output a value for a covered base? question Looking for clarification on inputs and/or outputs
#200 by Ge0rges was closed Jun 9, 2024 updated Jun 9, 2024
3
Automated filter threshold set to 1 for pileup and questions about thresholding question Looking for clarification on inputs and/or outputs troubleshooting workflow and data preparation questions
#198 by kylepalos was closed Jun 6, 2024 updated Jun 6, 2024
4
Output tsv has some minor code duplication issues in find-motif code part. bug Something isn't working build-available custom build produced for fix.
#195 by bgdga was closed Jun 4, 2024 updated Jun 4, 2024
4
Error writing results of find-motifs
#197 by SorenHeidelbach was closed Jun 4, 2024 updated Jun 4, 2024
1
p values using regions option question Looking for clarification on inputs and/or outputs
#188 by lucy924 was closed May 28, 2024 updated May 28, 2024
3
Error! should be at least 1 contig
#189 by james-e-barrett was closed May 27, 2024 updated May 27, 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 updated May 23, 2024
6
Calling 5hmC question Looking for clarification on inputs and/or outputs
#186 by KevDonn was closed May 23, 2024 updated May 23, 2024
4
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