MethylCoder
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Application data |
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| Created by | Pedersen BS |
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| Biological application domain(s) | Genomics, Sequencing, DNA methylation, Epigenomics |
| Principal bioinformatics method(s) | Read mapping, Bisulfite mapping |
| Technology | Illumina |
| Created at | UC Berkeley |
| Maintained? | Yes |
| Input format(s) | FASTQ, FASTA |
| Output format(s) | binary, TXT, SAM |
| Programming language(s) | Python, C |
| Licence | BSD |
| Operating system(s) | Linux, Linux 64, Mac OS X |
Summary: Pipeline for fast, simple processing of BiSulfite-treated reads into methylation data. Includes scripts for analysis and visualization. In addition to a binary output, the direct output of methylcoder is a text file that indicates per-nucleotide methylation context (CG/CHG/CHH) and methylation levels (both coverage and C-T conversions)
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Pipeline for fast, simple processing of BiSulfite-treated reads into methylation data. Includes scripts for analysis and visualization. In addition to a binary output, the direct output of methylcoder is a text file that indicates per-nucleotide methylation context (CG/CHG/CHH) and methylation levels (both coverage and C-T conversions). The direct output of methylcoder is a text file that looks like
#chrom mt bp c t 1 3 1354 0 1 1 3 1358 0 1 1 3 1393 0 1 1 3 1394 0 1 1 3 1402 0 1 1 3 1409 0 1
where columns are reference seqid methylation context (type) basepair location(bp) number of reads where a (c)ytosine was unconverted, number of reads where where a cytosine was converted to (t)hymine. Making methylation at every methylable basepair easily calculated as c / (c + t).
In addition, a SAM file with corrected positions and sequences is created for use with other bioinformatics packages.
Can use either bowtie or gsnap as the aligner. Example invocation:
methylcoder \
--bowtie /usr/local/src/bowtie-0.12.5/ \
--reference hu19.fa \
--extra-args "-m 1 -e 100" \
reads/r_1.fastq reads/r_2.fastq
Links
- MethylCoder [ edit link ]
References
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