as UCSC custom track mapping_to_ucsc.py $out_file1 $input $chr_col $coord_col $track.track_type #if $track.track_type == "coverage" or $track.track_type == "both" $track.coverage_col "${track.cname}" "${track.cdescription}" "${track.ccolor}" "${track.cvisibility}" #end if #if $track.track_type == "snp" or $track.track_type == "both" "${track.sdescription}" "${track.svisibility}" $track.col2 #end if SNPs Read coverage Both Black Red Green Blue Magenta Cyan Gold Purple Orange Pink Dark Chocolate Olive green Dense Full Pack Squish Hide Dense Full Pack Squish Hide Black Red Green Blue Magenta Cyan Gold Purple Orange Pink Dark Chocolate Olive green Dense Full Pack Squish Hide Dense Full Pack Squish Hide .. class:: infomark **What it does** This tool turns mapping data generated by short read mappers into a format that can be displayed in the UCSC genome browser as a custom track. ----- .. class:: warningmark **Note** This tool requires the mapping data to contain at least the following information: chromosome, genome coordinate, read nucleotide (if option to display is SNPs), read coverage (if option to display is Read coverage). ----- **Example** For the following Mapping data:: #chr g_start read_id read_coord g_nt read_nt qual read_coverage chrM 1 1:29:1672:1127/1 11 G G 40 134 chrM 1 1:32:93:933/1 4 G A 40 134 chrM 1 1:34:116:2032/1 11 G A 40 134 chrM 1 1:39:207:964/1 1 G G 40 134 chrM 2 1:3:359:848/1 1 G C 40 234 chrM 2 1:40:1435:1013/1 1 G G 40 234 chrM 3 1:40:730:972/1 9 G G 40 334 chrM 4 1:42:1712:921/2 31 G T 35 434 chrM 4 1:44:1649:493/1 4 G G 40 434 running this tool to display both SNPs and Read coverage will return the following tracks, containing aggregated data per genome co-ordinate:: track type=wiggle_0 name="Coverage Track" description="User Supplied Track (from Galaxy)" color=0,0,0 visibility=1 variableStep chrom=chrM 1 134 2 234 3 334 4 434 track type=wiggle_0 name="Track A" description="User Supplied SNP Track (from Galaxy)" color=255,0,0 visibility=1 variableStep chrom=chrM 1 2 track type=wiggle_0 name="Track T" description="User Supplied SNP Track (from Galaxy)" color=0,255,0 visibility=1 variableStep chrom=chrM 4 1 track type=wiggle_0 name="Track G" description="User Supplied SNP Track (from Galaxy)" color=0,0,255 visibility=1 variableStep chrom=chrM 1 2 2 1 3 1 4 1 track type=wiggle_0 name="Track C" description="User Supplied SNP Track (from Galaxy)" color=255,0,255 visibility=1 variableStep chrom=chrM 2 1