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methylartist-tests

Test data and examples for methylartist (https://github.com/adamewing/methylartist).

Run all examples using run_tests.sh and compare to output below.

Example using scoredist:

methylartist scoredist -n 300000 -d data/MCF7_ATCC.sample.megalodon.db,data/MCF7_ECACC.sample.megalodon.db -m m

scoredist

Example using segmeth:

methylartist segmeth -d MCF7.example.data.txt -i MCF7.example.segments.bed -p 8

Yields a file: MCF7.example.segments.MCF7.example.data.segmeth.tsv

Various segplot examples:

methylartist segplot -s MCF7.example.segments.MCF7.example.data.segmeth.tsv -c LOW,MED1,MED2,HIGH -v --palette magma 
methylartist segplot -s MCF7.example.segments.MCF7.example.data.segmeth.tsv -c LOW,MED1,MED2,HIGH -v --palette magma -a
methylartist segplot -s MCF7.example.segments.MCF7.example.data.segmeth.tsv -c LOW,MED1,MED2,HIGH -g --palette magma
methylartist segplot -s MCF7.example.segments.MCF7.example.data.segmeth.tsv -c LOW,MED1,MED2,HIGH -g --palette magma -a

segplot1 segplot2 segplot3 segplot4

Example using locus:

methylartist locus -d MCF7.example.data.txt -i chr19:56172382-56187168 --samplepalette crest -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes

locus

Example using locus with methylation calls stored in a .bam file using MM and ML tags, plus some other features:

methylartist with command: /home/taewing/miniconda3/bin/methylartist locus -b data/MCF7_ATCC.modification_tags.bam,data/MCF7_ECACC.modification_tags.bam -i chr19:56172382-56187168 --samplepalette cubehelix -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes --ref data/Homo_sapiens_assembly38.fasta.gz --motif CG --show_transcripts --smoothed_csv test.csv --exonheight 0.6 --panelratios 2,5,1,3,3

locus_bam

Example using locus with phased sample (HP and PS tags):

methylartist locus -d MCF7.example.data.txt -i chr19:56810076-56870725 -l 56835376-56840476 -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --genes PEG3 --samplepalette viridis --phased --maskcutoff 0

locus_phased

Example using region to plot a 2 Mbp segment:

methylartist region -d MCF7.example.data.txt -i chr19:55810082-57840726 -n CG -r /home/data/ref/hg38/Homo_sapiens_assembly38.fasta -p 8 -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --genepalette viridis --samplepalette magma

region

Loading and display of C/U substitution based data (e.g. BS-seq or EM-seq)

Note locus may take a long time to plot reads, a fix is pending.

methylartist db-sub -b NA12878.EMSEQ.GAPDH.bam -d NA12878.EMSEQ.GAPDH.db

cat sub_test.data.txt
NA12878.EMSEQ.GAPDH.bam NA12878.EMSEQ.GAPDH.db

methylartist locus -d sub_test.data.txt -i chr12:6,517,169-6,555,718 -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes --panelratios 5,5,1,3,3

sub