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BismarkAlign

Performs alignment of bisulfite sequencing data in addition to deduplication and methylation extraction using Bismark Bisulfite Mapper

Version 1.0
Bundle sequencing
Categories Analysis
Authors Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI)
Issue tracker View/Report issues
Requires bismark ; samtools ; bowtie ; bowtie2 ; installer (bash)
Source files component.xml BismarkAlign.sh
Usage Example with default values

Inputs

Name Type Mandatory Description
reads SequenceSet Mandatory Input reads in fastq or fasta format
refGenome BinaryFolder Mandatory The folder containing the converted reference genome. The conversion can be performed using bismark_genome_preparation tool.
mates SequenceSet Optional Input mates in fastq or fasta format

Outputs

Name Type Description
methylationCalls CSV Methylation calls in CpG context. For other contexts, check bismark documentation and include appropriate parameters in extractExtra parameter. The CSV contains the following columns: chr, position, strand, coverage, MethC.
bedGraph BED BedGraph output for methylation calls in CpG context. For other contexts, check bismark documentation and include appropriate parameters in extractExtra parameter.
alignment BAM Aligned reads in BAM format. If the parameter dupRemoval is set to true, this output will be deduplicated.
Mbias BinaryFile M-bias file reporting methylation percentage at different positions of reads in different contexts.
report HTMLFile The report of alignment, methylation extraction and deduplication (if performed).
analysis BinaryFolder Folder containing all produced files other than outputs.

Parameters

Name Type Default Description
alignExtra string "" Extra flags to be passed to the align function. Check bisrmak documentation.
aligner string "bowtie2" The aligner to be used, can be "bowtie" or "bowtie2". The input refGenome should be constructed with the same aligner.
deleteNonCpG boolean true Set true for deleting non-CpG context files.
directional boolean true Set true for directional BS-Seq libraries. In directional alignment, reads will be aligned to the original top and bottom strands. In non-directional alignment, reads will be aligned to original top and bottom strands in addition to the strands complementary to original top and bottom strands.
dupRemoval boolean true Set true for performing duplicate removal. Do not use with RRBS data!
extract boolean true Whether to extract methylation from bam file.
extractExtra string "" Extra flags to be passed to the methylation extraction function. Check bismark documentation.
ignoreR1 int 1 Ignore the first "number" of bp from the 5’ end of reads when processing the methylation call string.
ignoreR2 int 2 Ignore the first "number" of bp from the 5’ end of mates when processing the methylation call string. (only with paired end).
inputFormat string "fastq" Input format, fastq or fasta.
paired boolean true Set true for paired-end reads.

Test cases

Test case Parameters IN
reads
IN
refGenome
IN
mates
OUT
methylationCalls
OUT
bedGraph
OUT
alignment
OUT
Mbias
OUT
report
OUT
analysis
case1 properties reads refGenome (missing) (missing) (missing) (missing) (missing) (missing) (missing)

aligner=bowtie,
paired=false,
extractExtra=--buffer_size 50%,
extract=false

case2 properties reads refGenome mates (missing) (missing) (missing) (missing) (missing) (missing)

aligner=bowtie2,
directional=false,
dupRemoval=false,
alignExtra=--maxins 1000,
extract=true


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