Bismark

Bismark copied to clipboard

Bismark genome preparation issue

3

Hi Felix, Newbie to Bioinformatics here. I'm trying to build an index for my reference genome from Ubuntu using the following script:  I've been able to run...

lahyusof

Hi, After running the alignment step, the output results left me a bit confused. The value for 'C methylated in Unknown context (CN or CHN): 48.4%' is surprisingly high. What...

Ldabao233

Unexpected large number of CpG sites

4

I have a methylation data sequenced with a methylome panel. However, when I look into the coverage/bedgraph file generated by `bismark_methylation_extractor`, the number of CpG sites exceed than the panel...

Larrycpan

Filtering mapping qulaity

2

Hello, Is it recommended to filter the bam files after aligning with bismark according to the mapping quality, before extracting the methylation? There are mapped reads with mapping quality of...

reg321

bismark_methylation_extractor

6

Hi, I recently used the following command to extract methylation information for genome CpG sites from a BAM file. However, I noticed that some of the sites in the output...

zhangqc723

bismark_methylation_extractor samtools view: writing to standard output failed: Broken pipe

4

bismark_methylation_extractor -p --comprehensive --bedGraph --counts --cytosine_report --buffer_size 30G --report --parallel 8 --genome_folder ../reference 1_bismark_bt2_pe.deduplicated.bam -o ./ The above is my running code, and the log file is shown below **********************************...

caaswangzhen

Unable to read file magic number

2

**When I use bismark to map DNA methylation data, the log file shows this error. At the same time, the mapping is also very low. error infotmation:** Unable to read...

GaojieLi-dot

Better Handling of Bismark2Report Uninitialized Error due to missing nucleotide key in nucleotide.stats report

1

Hi @FelixKrueger, There are cases where the `nucleotide_stats` does not generate the full list of nucleotide headers as expected by the bismark2report script. Below I post the source ode causing...

rhondene

Low Mapping efficiency

9

Hi, Felix. I'm so sorry to bother you again. I have WGBS data from the same batch for two species (Accel Swift data) and have already trimmed it using the...

Marh32

Issue with Alignment Results Using Soft-Masked Genome in Bismark

3

I am currently conducting Whole Genome Bisulfite Sequencing (WGBS) data analysis using Bismark and plan to utilize a soft-masked genome, where all repetitive and low-complexity regions are marked with lowercase...

Chanspace