Song-Liyang / tasmark

Bioinformatic software for TAPS DNA methylation sequencing

tasmark

A Bioinformatic Toolkit for TAPS DNA Methylation Sequencing
v0.1.0 by Song Liyang
https://github.com/Song-Liyang/tasmark
This program was written by Song Liyang ([e-mail]), Peking University.
This program was built on source code from Bismark 0.2.0 by Felix Krueger

Usage

Download tasmark file and execute(don't forget chmod +x) directly. Tasmark need Perl, Bowtie2 and Samtools.

USAGE: tasmark [options] <genome_folder> --index <index_name> {-1 <mates1> -2 <mates2> | <singles>}

<genome_folder>
The path to the folder containing the reference genome .fa or fa.gz

--index <index_name>
path/to/bowtie2/index/your_basename Tasmark will search for your_basename.1.bt2.Tasmark need existing bowtie2_builder index instead of extra "genome preparation" step.

<reads> or -1 <reads1> -2 <reads2>
fasta file or fastQ file of single_end(read1 only) or paired_end sequencing data.

-o Output directoy (current directoy default).
--multicore <int> Run on multiple CPUs.
--non_directional Library prep with multiple rounds of random primming just after C->T conversion.

Other options is almost same to Bismark. Use --help for detail.

Output

Bismark style sam files with following info (tab separate).

1.QNAME (seq-ID)
2.FLAG ( bowtie2 provid)
3.RNAME (chromosome name)
4.POS (start position)
5.MAPQ (only calculated for Bowtie 2, always 255 for Bowtie)
6.CIGAR
7.RNEXT
8.PNEXT
9.TLEN
10.SEQ (forward strand)
11.QUAL (Phred33 scale)
12.NM-tag (hemming distance to the reference)
13.MD-tag (base-by-base mismatches to the reference)
14.XM-tag (methylation call string,forward strand)
15.XR-tag (read conversion state for the alignment,NN , CT or GA)
16.XG-tag (genome conversion state for the alignment, alwaysNN)

For methylation call string (XM-tag), same like Bismark.

• z - C in CpG context - unmethylated
• Z - C in CpG context - methylated
• x - C in CHG context - unmethylated
• X - C in CHG context - methylated
• h - C in CHH context - unmethylated
• H - C in CHH context - methylated
• u - C in Unknown context (CN or CHN) - unmethylated
• U - C in Unknown context (CN or CHN) - methylated
• . - not a C or irrelevant position

tasmark_methylation_extractor extract methylation call to bed file, same function in bismark. usage: ./tasmark_methylation_extractor yoursample.sam
use --bedgraph to make a cov file (make sure tasmark2bedGraph has been downloaded).