Bismark

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Bowtie2 index faulty or non existant: bismark fails to run

2

Dear Felix, Greetings! I have been trying to run bismark (Bismark-0.23.1) for a paired end data for hg38. The genome preparation for reference hg38.fa gives me 5 files as output...

guruprasadh1996

bismark failing

3

I have human WGBS data and would like to use bismark to align the data, however, I keep getting this error message: scaffolds/contigs/chromosomes frequently encountered errors with pre-sorting reads to...

alyzas

Unexpected combination of read and genome conversion: /

5

Hi, Thanks for providing such a useful tool for DNA methylation analysis. Recently, I used the bismark_methylation_extractor to extract methylation information from a sorted bam file (which was generated by...

ccmeth

Using bed file

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Hi Felix, Is there any way to use a BED file to make the alignment (or methylation extraction) to concentrate on a specific range of regions. Many thanks

muntajihad

More alignments to sequence when included in whole genome than to the sequence alone

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Hi Felix, We have recently started analysing publicly-available single-end RRBS data from an organism we had never considered in the past. We are mostly interested in the ribosomal DNA (rDNA),...

franrodalg

Bismark Alignment Inquiry

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Hi Felix, I have a couple of questions regarding Bismark. I'm sorry if they are stupid questions; I am fairly new to WGBS data and Bismark analysis (or to bioinformatics...

KeemAntonio

Number of bisulfite transformed reads are not equal between Reads 1 and 2

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Dear Bismark Author, I was running my data with the bismark tool and i got the error message below. the version of bismark is: version v0.24.2 and the code i...

itsjoeka

Bismark Extract failed always ran out of memory after 8hrs.

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Bismark_mapping Failed, Run time 08:18:26, OUT_OF_MEMORY. Please see code bismark --genome_folder genomes/bismark -o bam/ --non_directional --parallel 8 --score_min L,-0.6,-0.6 -1 trimmed/${base1}_val_1.fq.gz -2 trimmed/${base2}_val_2.fq.gz What am I doing wrong? I am...

RachaelAjayi

pipe with bismark_methylation_extractor

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I wonder if it is possible to use pipe as input to bismark_methylation_extractor instead of file? something like samtools view bam.bam|head -1| bismark_methylation_extractor

jksr

Multi-mapping reads and low mapping efficiency

3

I am currently using Bismark to analyze DNA methylation data from root/nodule samples from a legume plant species and am facing issues regarding multi-mapping reads and low mapping efficiencies. My...

hAmbreen