FelixKrueger Bismark issues

FelixKrueger / Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

http://felixkrueger.github.io/Bismark/

GNU General Public License v3.0

394 stars 103 forks source link

issues

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Very low mapping efficiency in Bismark

#715 cuteelephant closed 1 week ago
2
CX.report Inquiry

#714 RosalynLiu885 closed 2 weeks ago
1
Low Mapping efficiency

#713 Marh32 opened 3 weeks ago
9
bismark(err): bowtie2-align died with signal 13 (pipe)

#712 wydsqgg524 opened 3 weeks ago
1
Better Handling of Bismark2Report Uninitialized Error due to missing nucleotide key in nucleotide.stats report

#711 rhondene opened 3 weeks ago
1
Question about Bismark's Handling of Mismatches and Deletions

#710 hmu-youbai closed 1 month ago
1
question about mapping efficiency

#709 Marh32 closed 1 month ago
7
Forward read data look great, paired end and reverse reads look erroneous

#708 robertocnava opened 1 month ago
2
Speed up merge_individual_BAM_files

#707 MilosCRF opened 1 month ago
4
SNAKEMAKE wrapper: How to add multicore?

#706 kenji-yt opened 1 month ago
1
Issue with Alignment Results Using Soft-Masked Genome in Bismark

#705 Chanspace opened 1 month ago
3
Visualizing the CpG, CHG and CHH in Seqmonk

#704 lahyusof opened 1 month ago
1
Query about including C in unknown context when calculating methylation proportions

#703 lahyusof closed 1 month ago
1
Terms used in reports

#702 gevro closed 1 month ago
1
Help with interpretation of M-bias plot

#701 xinyun-stacy-li closed 1 month ago
2
Getting strand information from/for bedGraph/coverage files

#700 jonasbucherETH opened 2 months ago
1
Bismark silently outputs incorrect results when UMIs are added using Illuminas bcl-convert

#699 lars-work-sund opened 2 months ago
7
Failed to create directory/file when path has space: Exit 141

#698 llrs closed 2 months ago
4
[help] Can Bismark handle diploid reference genome please?

#697 lizhe-gis opened 2 months ago
2
[Question] Questions about adding new aligners

#696 YuanfengZhang closed 2 months ago
2
the error when dedup the sam when use the bismak

#695 Jiangjiangzhang6 opened 2 months ago
1
directional and nondirectional

#694 iranianuser closed 3 months ago
6
Bismark2summary not working for output with hisat2

#693 JingranZhuo closed 3 months ago
6
index of genome faulty or non-existant

#692 iranianuser closed 3 months ago
5
deduplicate_bismark problem

#691 iranianuser closed 3 months ago
4
ambiguous results in .bam file

#690 iranianuser closed 3 months ago
3
bismark for human genome

#689 iranianuser closed 4 months ago
3
Issue with Perl in filter_non_conversion

#688 edogiuili closed 4 months ago
4
Dose it necessary to place reads in working directory?

#687 iranianuser closed 4 months ago
1
Use SRR files with .rar (ziped) format

#686 iranianuser opened 4 months ago
1
Bismark genome preparation issue

#685 lahyusof closed 1 month ago
3
Differences in bismark convertion result

#684 RubioB closed 4 months ago
1
bismark runs to an error when I try to run it using nextflow

#683 Ephantus-Wambui closed 4 months ago
4
Parent process: Failed to build index

#682 yangjw1996 closed 4 months ago
3
Expected unique alignment %

#681 gevro closed 5 months ago
2
help combining bismark pipeline with methylated UMIs

#680 shawpa opened 5 months ago
8
Correcting low % methylated regions

#679 gevro closed 5 months ago
4
How to extract methylation levels according to bam file

#678 myoucchent closed 5 months ago
6
Analyzing spike in control performance

#677 gevro closed 5 months ago
2
Low unique alignment %

#676 gevro closed 5 months ago
8
Confusion on how coverage is estimated

#675 RJDan closed 5 months ago
4
Very low mapping efficiency

#674 gevro closed 5 months ago
4
Spiky position in the M-Bias plot

#673 neolithlee opened 5 months ago
5
Issue with bismark_genome_prep

#672 maf222 opened 5 months ago
7
Execution Error

#671 KayaHarper closed 5 months ago
9
Bismark Alignment very slow

#670 Nitin123-4 closed 4 months ago
11
CpG count query

#669 MarkOEze closed 2 months ago
6
FATAL ERROR in extractor

#668 WYChen-penguin opened 7 months ago
5
Some trouble with the FastQC report

#667 Citrusyh opened 7 months ago
3
Bismark methylation extractor's bedGraph output returning ~50 million CpGs for WGBS?

#666 JanmajaySingh closed 7 months ago
9