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.

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