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art - Online in the Cloud

Run art in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command art that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


art - Artemis genome browser and annotation tool

SYNOPSIS


art [options] SEQUENCE_FILE [+FEATURE_FILE...]

OPTIONS


SEQUENCE_FILE An EMBL, GenBank, FASTA, or GFF3 file
FEATURE_FILE An Artemis TAB file, or GFF file

-options FILE Read a text file of options from FILE
-debug Run using the debugging JVM instead
-fast | -fast64 Use the FastVM (hp Tru64 UNIX) with 32/64 bit
pointers

-Dblack_belt_mode=? Keep warning messages to a minimum [true,false]
-Doffset=XXX Open viewer at base position XXX [integer >= 1]
-Duserplot=FILE[,FILE2] Open one or more userplots
-Dloguserplot=FILE[,FILE2] Open one or more userplots, take log(data)
-Dbam=FILE[,FILE2,...] Open one or more BAM, VCF or BCF files
-DbamClone=n Open all BAMs in multiple (n > 1) panels
-Dbam[1,2,..]=FILE[,FILE2,..] Open BAMs in separate panels
-Dshow_snps Show SNP marks in BamView
-Dshow_snp_plot Open SNP plot in BamView
-Dshow_cov_plot Open coverage plot in BamView
-Dshow_forward_lines=? Hide/show forward frame lines [true,false]
-Dshow_reverse_lines=? Hide/show reverse frame lines [true,false]
-Dchado="h:p/d?u" Get Artemis to open this CHADO database
-Dread_only Open CHADO database read-only

EXAMPLES


% art AJ006275.embl
% art contigs.fa +annotation.gff +islands.tab
% art -Dblack_belt_mode=true -Dbam=ecoli_hiseq.bam E_coli_K12.gbk
% art -Duserplot=repeatmap.plot,geecee.plot Plasmid.gff3

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