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

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issues

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Expected unique alignment %

#681 gevro closed 1 hour ago
2
help combining bismark pipeline with methylated UMIs

#680 shawpa opened 6 days ago
3
Correcting low % methylated regions

#679 gevro closed 1 week ago
4
How to extract methylation levels according to bam file

#678 myoucchent closed 1 week ago
6
Analyzing spike in control performance

#677 gevro closed 1 week ago
2
Low unique alignment %

#676 gevro closed 1 week ago
8
Confusion on how coverage is estimated

#675 RJDan closed 1 week ago
4
Very low mapping efficiency

#674 gevro closed 2 weeks ago
4
Spiky position in the M-Bias plot

#673 neolithlee opened 2 weeks ago
3
Issue with bismark_genome_prep

#672 maf222 opened 2 weeks ago
7
Execution Error

#671 KayaHarper closed 2 weeks ago
9
Bismark Alignment very slow

#670 Nitin123-4 opened 1 month ago
7
CpG count query

#669 MarkOEze opened 1 month ago
4
FATAL ERROR in extractor

#668 WYChen-penguin opened 2 months ago
5
Some trouble with the FastQC report

#667 Citrusyh opened 2 months ago
3
Bismark methylation extractor's bedGraph output returning ~50 million CpGs for WGBS?

#666 JanmajaySingh closed 2 months ago
9
Update deduplication.md

#665 josefoviedo closed 3 months ago
2
mbias plot methylation rate fluctuations

#664 ertiaM closed 3 months ago
4
Minimum conversion efficiency for filter_non_conversion

#663 gevro closed 3 months ago
1
Bismark Extract failed always ran out of memory after 8hrs.

#662 RachaelAjayi opened 3 months ago
4
alignment problem with reference genome

#661 Silvia-Giorgia-Signorini closed 3 months ago
5
pipe with bismark_methylation_extractor

#660 jksr opened 3 months ago
1
Can deduplicate_bismark (the component of bismark) script distinguish single-end/paired-end BAM/SAM Bismark files directly ?

#659 changchuanjun closed 4 months ago
6
Is it necessary to execute command (samtools sort -n) before run Deduplication?

#658 changchuanjun closed 4 months ago
2
Number of bisulfite transformed reads are not equal between Reads 1 and 2

#657 itsjoeka opened 4 months ago
6
Multi-mapping reads and low mapping efficiency

#656 hAmbreen opened 4 months ago
3
Generating cytosine report

#655 desmodus1984 closed 3 months ago
15
Bismark Alignment Inquiry

#654 KeemAntonio opened 4 months ago
10
Incomplete Documentation regarding expected outputs

#653 VasLem closed 4 months ago
6
Bismark issues 0.24.2

#652 NeGomics opened 4 months ago
7
Bismark Version: v0.24.2 Issue

#651 NeGomics closed 4 months ago
1
Is are ways to decrease the memory requirement of coverage2cytosine at the expense of computation time?

#650 onurcanbektas opened 5 months ago
2
advice on data analysis

#649 riyabelani opened 5 months ago
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 wangguiqian closed 5 months ago
65
question about difference of detected cytosine sites between CX_report.txt and bismark.cov.gz

#647 yinzhuo0322 opened 6 months ago
4
MAPQ Filtering Post Alignment Using --local Parameter

#646 allenloong opened 6 months ago
2
bismark bowtie2

#645 yhj-j opened 6 months ago
3
Methylation extractor stuck

#644 xbarvazx opened 6 months ago
4
how do bismark deal with those softclip reads which could be alinged to a reference partially?

#643 feihongloveworld closed 6 months ago
1
about unmapped reads

#642 feihongloveworld closed 6 months ago
3
Mapping Efficiency is low

#641 AmrSaadeldin closed 6 months ago
4
bsseq::read.bismark() input - reference error

#640 desmodus1984 closed 7 months ago
3
Extremely low mapping efficiency using bowtie2 and reference genome with many scaffolds

#639 LauraRt1 closed 4 months ago
11
Linear memory growth during alignment.

#638 iromeo opened 7 months ago
3
bismark aligning comma-separated list of fastq files stops after first sample finished

#637 chuddy-ibk closed 7 months ago
1
How to extract CpG level for IGV plot

#636 abearab closed 8 months ago
5
More than 29 millions rows in the coverage file

#635 demis001 closed 8 months ago
7
Throttle total memory and CPU usage for large WGBS datasets

#634 abearab closed 8 months ago
2
CRISPRoff methylation specificity analysis

#633 abearab closed 8 months ago
4
[Questions] Loci present in the bedgraph file and coveage file are not present in cytosine_report

#632 VicSkuldy closed 8 months ago
1