Calculate DNA methylation level
Calmeth
Calculate DNA methylation level from alignment files, you can obtained single-base cytosine DNA methylation results, and the chromosome region DNA methylation levels files.
An example usage is:
with bam file:
calmeth [options] -g genome.fa -b alignment.sort.bam -m output.methrario.txt
with sam file:
calmeth [options] -g genome.fa -i alignment.sort.sam -m output.methrario.txt
Important
The bam or sam file MUST sorted by samtools sort.
Paramaters
[ Main paramaters ] |
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-m/--methratio |
[MethFileNamePrefix] Predix of methratio output file |
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--genome/-g |
Name of the genome mapped against, MUST build index first Build index |
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-i/--input |
Sam format file, sorted by samtools sort. |
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-b/--binput |
Bam format file, sorted by samtools sort. |
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-Q [int] |
caculate the methratio while read QulityScore >= Q. default:20 |
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-n [float] |
Number of mismatches, default 0.06 percentage of read length. [0-1] |
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-c|--coverage |
>= <INT> coverage. default:4 |
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-nC |
>= <INT> Cs per region. default:1 |
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-R/--Regions |
Bins for DMR caculate , default 1000(1kb) . |
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--binsfile |
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DNA methylation level distributions in chrosome, default output file: {Prefix}.methBins.txt |
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-s/--step |
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Chrosome using an overlapping sliding window of 100000bp at a step of 50000bp. default step: 50000(bp) |
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-r/--remove_dup |
REMOVE_DUP, default:true |
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-f|--sam [outfile] |
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f for sam format outfile contain methState. |
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--sam-seq-beforeBS |
Converting BS read to the genome sequences. |
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--help/-h |
Print help |
Output files
1. prefix.methratio.txt
2. prefix.methBins.txt
3. prefix_Region.CG/CHG/CHH.txt
4. prefix.mCdensity.txt
5. prefix.mCcatero.txt
Output file format
1. methratio
Chromosome Loci Strand Context C_count CT_count methlevel eff_CT_count rev_G_count rev_GA_count MethContext 5context
# ex. Chr1 61 + CHH 3 11 0.286364 10.5 20 21 hU ATCTT
# C_count The number of C in this base pair.
# CT_count The number of coverage in this base pair.
# eff_CT_count Adjust read coverage based on opposite strand.
# rev_G_count The number of G in the reverse strand.
# rev_GA_count The number of coverage in the reverse strand.
# MethContext M/Mh/H/hU/U, M means the methylation level ≥ 80%, etc
2. methBins
Chrom BinIndex methlevel context
# ex. Chr1 1 0.113674 CG
# The BinIndex is defined by -s paramater in calmeth.
# This file can be used for visualization the DNA methylation level acorss the chromosome.
3. Region
chrom regionStart strand context c_count ct_count
# ex. Chr1 1001 + CG 1 227
# The bins methylation level output file (BS.mr_Region.C*.txt) can be used to do DMR detection.
4. mCdensity
CG/CHG/CHH C count in [0, 1%) [1%, 2%) ... [49%, 50%) ... [99%, 100%]
# According to the DNA methylation level, the number of cytosine sites at different methylation levels was counted from 0 to 100.
5. mCcatero
Average DNA methylation level including mC, mCG and other states.
Tip
For feature requests or bug reports please open an issue on github.