Difference between revisions of "Calling card"
(Created page with "* Calling card track is a new type of track invented by [http://genetics.wustl.edu/rmlab/ Rob Mitra's lab], since version 46 it was integrated to the browser. == Format the D...") |
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Revision as of 09:37, 9 March 2018
- 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.
