Calling card

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  • Calling card track is a new type of track invented by Rob Mitra's lab, since version 46 it was integrated to the browser.

Format the Data

Calling card data must be stored in a tab-delimited, plain text format. This format requires a minimum of four columns and can support up to six. The four required columns are CHROM, START, STOP, and COUNT, where COUNT refers to the number of reads for that insertion. The START and STOP columns can be either 0- or 1-indexed. The fifth and sixth columns are optional and represent STRAND and BARCODE, respectively. Here is an example of a four-column calling card file:

chr1    41954321        41954325        1
chr1    41954321        41954325        18
chr1    52655214        52655218        1
chr1    52655214        52655218        1
chr1    54690384        54690388        3
chr1    54713998        54714002        1
chr1    54713998        54714002        1
chr1    54713998        54714002        13
chr1    54747055        54747059        1
chr1    54747055        54747059        4
chr1    60748489        60748493        2

Here is an example of a six-column calling card file:

chr1    51441754        51441758        1       -       CTAGAGACTGGC
chr1    51441754        51441758        21      -       CTTTCCTCCCCA
chr1    51982564        51982568        3       +       CGCGATCGCGAC
chr1    52196476        52196480        1       +       AGAATATCTTCA
chr1    52341019        52341023        1       +       TACGAAACACTA
chr1    59951043        59951047        1       +       ACAAGACCCCAA
chr1    59951043        59951047        1       +       ACAAGAGAGACT
chr1    61106283        61106287        1       -       ATGCACTACTTC
chr1    61106283        61106287        7       -       CGTTTTTCACCT
chr1    61542006        61542010        1       -       CTGAGAGACTGG

Your text file must be sorted by the first three columns. If your filename is example.ccf, you sort it with the following command: sort -k1V -k2n -k3n example.ccf > example_sorted.ccf

Note that you can have strand information without a barcode, but you cannot have barcode information without a strand column.