Pipeline
Tip
BatMeth2 can perform one click analysis or the following modules step by step:
tool |
input files |
main output file(s) |
main application |
---|---|---|---|
Single/Paired-end fastq/gz files |
alignment sam/bam file |
Perform DNA methylation level calculation and SNP/ASM detection |
|
BS-seq align sorted sam/bam file |
methratio file (loci/region) |
Perform DNA methylation visulization on chromosome, and diff analysis |
|
methration file from calmeth |
methlevel file on genes/TEs etc. |
DNA methylation profile or heatmap on genes/TEs/peak regions/etc. |
|
methration file from calmeth |
bigwig files (c/cg/chg/chh) |
Convert DNA methylation file to bigwig format. |
|
methy files from calmeth/methyGff |
methy profile/heatmap/boxplot |
visulization of DNA methylation across samples |
|
methration file from calmeth |
Diff methy cytosines/regions |
Perform Differential DNA methylation analysis |
BatMeth2 pipeline
An easy-to-use, auto-run package for DNA methylation analyses:
Raw reads:
BatMeth2 pipel --fastp ~/location/to/fastp \
-1 Raw_reads_1.fq.gz -2 Raw_read_2.fq.gz \
-g ./batmeth2index/genome.fa \
-o meth -p 8 --gff ./gene.gff
Or clean reads:
BatMeth2 pipel -1 Clean_reads_1.fq.gz -2 Clean_read_2.fq.gz \
-g ./batmeth2index/genome.fa \
-o meth -p 8 --gff ./gene.gff
You can always see all available command-line options via --help:
$ BatMeth2 --help
After the program runs successfully, a series of files with '- o' as prefix and DNA methylation level will be generated in the output directory. Please refer to the doc for the specific output file and format details.
In addition, there will be an HTML report file containing basic information and statistical results of data analysis.
BatMeth2 pipeline main parameters
Build index
Usage: (must run this step first)
Build index using for wgbs data
$ BatMeth2 index -g genomefile
Build index using for rrbs data
$ BatMeth2 index_rrbs -g genomefile
Main Alignment paramaters
[ Fastq Quality Conreol ] |
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--fastp |
fastp program location |
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If --fastp is not defined, the input file should be clean data. |
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[ Main paramaters ] |
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-o |
Name of output file prefix |
|
-O |
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Output of result file to specified folder, default output to current folder (./) |
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[ Aligners paramaters ] |
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-g |
Name of the genome mapped against |
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-i |
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Name of input file, if paired-end. please use -1, -2, input files can be separated by commas. eg. -1 readA.fq.gz,readB.fq.gz -2 .. |
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-1 |
Name of input file left end, if single-end. please use -i |
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-2 |
Name of input file left end |
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-p |
Launch <integer> threads |
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-n |
maximum mismatches allowed due to seq. errors [0-1] |
Calmeth paramaters
--Qual |
calculate the methratio while read QulityScore >= Q. default:20 |
|
--redup |
REMOVE_DUP, 0 or 1, default 1 |
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--region |
Bins for region meth calculate , default 1000bp. |
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-f |
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for sam format outfile contain methState. [0 or 1], default: 0 (dont output this file). |
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--coverage |
>= <INT> coverage. default: 4 |
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--binCover |
>= <INT> nCs per region. default: 3 |
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--chromstep |
>= <INT> nCs per region. default: 3 |
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Chromosome using an overlapping sliding window of 100000bp at a step of 50000bpdefault step: 50000(bp) |
MethyGff/Annoation paramaters
--gtf/--gff/--bed/--bed4/--bed5 |
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gtf / gff / bed files, bed: Chr start end; bed4: Chr start end strand; bed5: Chr start end id strand; |
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-d/--distance |
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DNA methylation level distributions in body and <INT>-bp flanking sequences. The distance of upstream and downstream. default:2000 |
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--step |
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Gene body and their flanking sequences using an overlapping sliding window of 5%of the sequence length at a step of 2.5% of the sequence length. So default step: 0.025 (2.5%) |
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-C |
<= <INT> coverage. default:1000 |
Output files
Output file format and details see "https://github.com/GuoliangLi-HZAU/BatMeth2/blob/master/output_details.pdf".<br>
Output report details see "https://www.dna-asmdb.com/download/batmeth2.html" .<br>
Tip
For feature requests or bug reports please open an issue on github.