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21 Open 592 Closed
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Issues list

Correcting low % methylated regions
#679 by gevro was closed Jun 24, 2024
4
How to extract methylation levels according to bam file
#678 by myoucchent was closed Jun 24, 2024
6
Analyzing spike in control performance
#677 by gevro was closed Jun 24, 2024
2
Low unique alignment %
#676 by gevro was closed Jun 24, 2024
7
Confusion on how coverage is estimated
#675 by RJDan was closed Jun 21, 2024
4
Very low mapping efficiency
#674 by gevro was closed Jun 15, 2024
4
Execution Error
#671 by KayaHarper was closed Jun 11, 2024
9
Bismark methylation extractor's bedGraph output returning ~50 million CpGs for WGBS?
#666 by JanmajaySingh was closed Apr 9, 2024
9
mbias plot methylation rate fluctuations
#664 by ertiaM was closed Mar 26, 2024
4
Minimum conversion efficiency for filter_non_conversion
#663 by gevro was closed Mar 14, 2024
1
alignment problem with reference genome
#661 by Silvia-Giorgia-Signorini was closed Mar 13, 2024
5
Can deduplicate_bismark (the component of bismark) script distinguish single-end/paired-end BAM/SAM Bismark files directly ?
#659 by changchuanjun was closed Mar 1, 2024
6
Is it necessary to execute command (samtools sort -n) before run Deduplication?
#658 by changchuanjun was closed Mar 1, 2024
2
Generating cytosine report
#655 by desmodus1984 was closed Mar 5, 2024
15
Incomplete Documentation regarding expected outputs
#653 by VasLem was closed Feb 16, 2024
6
Bismark Version: v0.24.2 Issue
#651 by NeGomics was closed Feb 13, 2024
1
The HISAT2 index of the C->T converted genome seems to be faulty (BS_CT.1.ht2 doesn't exist). Please run bismark_genome_preparation --hisat2 b
#648 by wangguiqian was closed Jan 9, 2024
65
how do bismark deal with those softclip reads which could be alinged to a reference partially?
#643 by feihongloveworld was closed Dec 14, 2023
1
about unmapped reads
#642 by feihongloveworld was closed Dec 7, 2023
3
Mapping Efficiency is low
#641 by AmrSaadeldin was closed Dec 7, 2023
4
bsseq::read.bismark() input - reference error
#640 by desmodus1984 was closed Nov 21, 2023
3
Extremely low mapping efficiency using bowtie2 and reference genome with many scaffolds
#639 by LauraRt1 was closed Feb 23, 2024
11
bismark aligning comma-separated list of fastq files stops after first sample finished
#637 by chuddy-ibk was closed Nov 9, 2023
1
How to extract CpG level for IGV plot
#636 by abearab was closed Nov 2, 2023
5
More than 29 millions rows in the coverage file
#635 by demis001 was closed Oct 27, 2023
7
ProTip! no:milestone will show everything without a milestone.