Bismark

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Spiky position in the M-Bias plot

5

  The data I used was processed by fastqc and Trim_galore. And it is processed by bismark, deduplicate_bismark and bismark_methylation_extractor as specified in the manual. As can be seen...

neolithlee

Issue with bismark_genome_prep

7

Hello there I am running into an issue while running the human genome on the test file below. After I do the genome prep I see these messages. I verified...

maf222

Bismark Alignment very slow

7

Hi Team, I am running Bismark with the below command. I can see it's really slow. bismark --bowtie2 -N 1 --parallel 4 $RESOURCES2/HG38/ -1 $Read1 -2 $Read2 --output_dir $PWD --temp_dir...

Nitin123-4

CpG count query

4

Hello, I have some DNA methylation data, which I prepared using EM-Seq and got around 236 million paired-end reads after sequencing on the Illumina NextSeq platform. I have some concerns...

MarkOEze

FATAL ERROR in extractor

5

I have read many closed issues with a similar problem: #211 #219 #360 I used the module already set up in the supercomputer (ver. 0.24.1). Here is one of the...

WYChen-penguin

Some trouble with the FastQC report

6

Hi Felix, I am sorry to trouble you. I’m having some trouble with the FastQC report and would like to ask you. 1. According to the “Per base sequence content”,...

Citrusyh

Bismark silently outputs incorrect results when UMIs are added using Illuminas bcl-convert

7

This is not really a bug as the documentation clearly states how deduplicate_bismark expects UMIs to be handled, but it is an easy mistake to make. As documented in deduplicate_bismark,...

lars-work-sund

[help] Can Bismark handle diploid reference genome please?

2

Dear Felix, Thank you so much for developing this great tool! I rely Bismark heavily for my research :) Recently we developed a haplotype-resolved diploid human genome, where one copy...

lizhe-gis

the error when dedup the sam when use the bismak

1

bismark  the map command : /bismark --genome_folder ../01.hap1 --hisat2 --non_directional -1 ../clean_ZHM1H.R1.fastq.gz -2 ../clean_ZHM1H.R2.fastq.gz -p 5 -L 30 -N 1 -o hap1 #--output_dir ./ --bam hap1_bismark_hisat2_pe.bam my friends, what's...

Jiangjiangzhang6

Use SRR files with .rar (ziped) format

1

Hello I had trouble with uploading my read files in a sever to do Bismark analysis cause they are so big (about 20 G). I compressed them with winRar and...

iranianuser