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FelixKrueger
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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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Update deduplication.md
#665
josefoviedo
closed
8 months ago
2
mbias plot methylation rate fluctuations
#664
ertiaM
closed
8 months ago
4
Minimum conversion efficiency for filter_non_conversion
#663
gevro
closed
8 months ago
1
Bismark Extract failed always ran out of memory after 8hrs.
#662
RachaelAjayi
opened
8 months ago
4
alignment problem with reference genome
#661
Silvia-Giorgia-Signorini
closed
8 months ago
5
pipe with bismark_methylation_extractor
#660
jksr
opened
8 months ago
1
Can deduplicate_bismark (the component of bismark) script distinguish single-end/paired-end BAM/SAM Bismark files directly ?
#659
changchuanjun
closed
8 months ago
6
Is it necessary to execute command (samtools sort -n) before run Deduplication?
#658
changchuanjun
closed
9 months ago
2
Number of bisulfite transformed reads are not equal between Reads 1 and 2
#657
itsjoeka
opened
9 months ago
6
Multi-mapping reads and low mapping efficiency
#656
hAmbreen
closed
4 months ago
3
Generating cytosine report
#655
desmodus1984
closed
8 months ago
15
Bismark Alignment Inquiry
#654
KeemAntonio
opened
9 months ago
10
Incomplete Documentation regarding expected outputs
#653
VasLem
closed
9 months ago
6
Bismark issues 0.24.2
#652
NeGomics
opened
9 months ago
7
Bismark Version: v0.24.2 Issue
#651
NeGomics
closed
9 months ago
1
Is are ways to decrease the memory requirement of coverage2cytosine at the expense of computation time?
#650
onurcanbektas
opened
9 months ago
2
advice on data analysis
#649
riyabelani
opened
10 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
10 months ago
65
question about difference of detected cytosine sites between CX_report.txt and bismark.cov.gz
#647
yinzhuo0322
opened
10 months ago
4
MAPQ Filtering Post Alignment Using --local Parameter
#646
allenloong
opened
10 months ago
2
bismark bowtie2
#645
yhj-j
opened
11 months ago
3
Methylation extractor stuck
#644
xbarvazx
opened
11 months ago
4
how do bismark deal with those softclip reads which could be alinged to a reference partially?
#643
feihongloveworld
closed
11 months ago
1
about unmapped reads
#642
feihongloveworld
closed
11 months ago
3
Mapping Efficiency is low
#641
AmrSaadeldin
closed
11 months ago
4
bsseq::read.bismark() input - reference error
#640
desmodus1984
closed
1 year ago
3
Extremely low mapping efficiency using bowtie2 and reference genome with many scaffolds
#639
LauraRt1
closed
9 months ago
11
Linear memory growth during alignment.
#638
iromeo
opened
1 year ago
3
bismark aligning comma-separated list of fastq files stops after first sample finished
#637
chuddy-ibk
closed
1 year ago
1
How to extract CpG level for IGV plot
#636
abearab
closed
1 year ago
5
More than 29 millions rows in the coverage file
#635
demis001
closed
1 year ago
7
Throttle total memory and CPU usage for large WGBS datasets
#634
abearab
closed
1 year ago
2
CRISPRoff methylation specificity analysis
#633
abearab
closed
1 year ago
4
[Questions] Loci present in the bedgraph file and coveage file are not present in cytosine_report
#632
VicSkuldy
closed
1 year ago
1
Bismark_methylation_extrcator coverage file
#631
shaghayeghsoudi
closed
1 year ago
2
High duplication percentage
#630
albert-ying
closed
1 year ago
2
merging dev for new release
#629
FelixKrueger
closed
1 year ago
0
High levels of non CpG methylation
#628
mikulenaitev
closed
1 year ago
1
XM:z tag , which one is Unknown context ?
#627
chufuyun
closed
1 year ago
4
Updated GC context program
#626
erlitzkin
closed
1 year ago
1
How to map to homologous chromosomes?
#625
ellisztamas
closed
1 year ago
3
A problem when running bismark using the test_R1.fastq.gz、test_R2.fastq.gz
#624
hazel914
closed
1 year ago
3
output file has only R1 pair end
#623
JHBI115
closed
1 year ago
5
Seeking assistance with the "bismark_methylation_extractor" command.
#622
dianzhiyong
closed
1 year ago
5
Getting GC context methylation report
#621
erlitzkin
closed
1 year ago
5
CX report
#620
ceromova
closed
1 year ago
1
Issue with bismark_methylation_extractor
#619
yingyin2019
closed
1 year ago
2
What to do in a case of low mapping efficiency ?
#618
Emm2342
closed
1 year ago
3
Update CHANGELOG.md
#617
FelixKrueger
closed
1 year ago
0
Update bismark
#616
FelixKrueger
closed
1 year ago
0
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