Bismark

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Disabled --no-discordant for structural variations

1

Hi Felix, > Alignments should not be really discordant unless something weird happened during the library preparation, or possibly if you have structural variation or translocations in your genome. We...

MimoriK

Minor size differences in output bam file

1

Hi @FelixKrueger I have three bam outputs generated with identical parameters and identical versions of Bismark and bowtie2 using a set of paired end trimmed inputs. Three parallel parameters were...

chasingdex

bismark_methylation_extractor

7

I'm a newbie ，doing bismark_methylation_extractor, why does the cov file have zero lines bismark_methylation_extractor -p \ --parallel 16 \ --bedGraph --counts \ --cytosine_report --report\ --CX \ --comprehensive \ --buffer_size 10G...

yy549159265

Methylation extractor

5

Dear @FelixKrueger, I have been using this pipeline for a while now but have not seen the output below when using methylation extractor. I am pretty sure that I have...

keroguynes

An error was reported in methylation extraction

4

Hello Felix I encountered two errors after running step 3: Sorting input file CpG_context_wwz-guo2_R1_bismark_bt2_pe.txt.chrChr01.methXtractor.temp by positions (using -S of 1500G) Died at /data01/masterHome/houtong/bismark/bismark2bedGraph line 487. Finished BedGraph conversion ... and...

shoutong263

Bismark mapping issue

1

Hi Developers, Thanks a lot for providing such a useful tool. When I used the bismark code, I met with a very strange issue that did not appear before. I...

ccmeth

Reverse Sequenced Reads

4

Hello! Recently I sequenced some methylation libraries, single end mode, in the reverse direction (from the i7 side). Is it correct to input the genome.fasta file as is and run...

suzziek

Error running bismark_genome_preparation

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I am running: `bismark_genome_preparation --path_to_aligner /my_path/bowtie2-2.5.0-mingw-x86_64/bowtie2-2.5.0-mingw-x86_64/ --verbose /my_path/RRBS/ ` And I get the following output just after step III launches: bowtie2-build-s does not exist, try running `[g]make bowtie2-build-s' Parent process:...

chrismahony

Add cytosine context methylation totals to docs

1

We currently don't seem to have a description of the context specific methylation totals in the new (and awesome) docs. More information on the report are [here](https://github.com/FelixKrueger/Bismark/issues/321).

FelixKrueger

the best downstream program used for analyzing Bismark ouputs

2

Hi @all, Do you have any recommended software used for downstream analyzing Bismark outputs, such as detecting regions of differential methylation, calculating methylation rate for targeted region, creating average methylation...

biozzq