Alignment

BatMeth2 align

Single-end-reads

DNA methylation sequencing single-end data alignment:

An example usage is:
    batmeth2 -g /data/index/genome/genome.fa -i Read.fq.gz -o outPrefix -p 10

Paired-end-reads

DNA methylation sequencing paired-end data alignment:

An example usage is:
    batmeth2 -g /data/index/genome/genome.fa -1 Read_R1_left.fq.gz -2 Read_R2_right.fq.gz\
    -o outPrefix -p 10

Parameters

[ Main paramaters ]

--inputfile/-i

bs-seq input fastq files, fastq format or gzip format

--genome/-g

Name of the genome mapped against, MUST build index first Build index

--outputfile/-o

Name of output file prefix

--threads/-p

Launch <integer> threads

--non_directional

Alignments to all four bisulfite strands will be reported. Default: OFF.

--insertsize/-s

inital insert size, default 600, will be aoto detected by input files

--std/-d

standard deviatiion of reads distribution, will aoto detected by input

--flanksize/-f

size of flanking region for Smith-Waterman

--swlimit

try at most <integer> sw extensions

--indelsize

indel size

--NoInDels/-I

not to find the indels result

--help/-h

Print help

Note: To use BatMeth2, you need to first index the genome with Build index.

Tip

For feature requests or bug reports please open an issue on github.