diff --git a/docs/cli_reference.rst b/docs/cli_reference.rst index 45001241..6ff8627f 100644 --- a/docs/cli_reference.rst +++ b/docs/cli_reference.rst @@ -139,12 +139,16 @@ hictk dump Matrix unit (ignored when file is not in .hic format). -t,--table TEXT:{chroms,bins,pixels,normalizations,resolutions,cells} [pixels] Name of the table to dump. - -r,--range TEXT [all] Excludes: --query-file + -r,--range TEXT [all] Excludes: --query-file --cis-only --trans-only Coordinates of the genomic regions to be dumped following UCSC-style notation (chr1:0-1000). - --range2 TEXT [all] Needs: --range Excludes: --query-file + --range2 TEXT [all] Needs: --range Excludes: --query-file --cis-only --trans-only Coordinates of the genomic regions to be dumped following UCSC-style notation (chr1:0-1000). - --query-file TEXT:(FILE) OR ({-}) Excludes: --range --range2 + --query-file TEXT:(FILE) OR ({-}) Excludes: --range --range2 --cis-only --trans-only Path to a BEDPE file with the list of coordinates to be fetched (pass - to read queries from stdin). + --cis-only Excludes: --range --range2 --query-file --trans-only + Dump intra-chromosomal interactions only. + --trans-only Excludes: --range --range2 --query-file --cis-only + Dump inter-chromosomal interactions only. -b,--balance TEXT [NONE] Balance interactions using the given method. --sorted,--unsorted{false} Return interactions in ascending order. --join,--no-join{false} Output pixels in BG2 format. diff --git a/docs/reading_interactions.rst b/docs/reading_interactions.rst index 7359c25f..39bc828d 100644 --- a/docs/reading_interactions.rst +++ b/docs/reading_interactions.rst @@ -106,3 +106,22 @@ Dump tables other than pixels: 5000 10000 ... + + +Dump cis or trans interactions only: + +.. code-block:: console + + user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1000 --cis-only --join + + chr2L 7000 8000 chr2L 7000 8000 1745 + chr2L 7000 8000 chr2L 12000 13000 1766 + chr2L 7000 8000 chr2L 17000 18000 1078 + ... + + user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1000 --trans-only --join + + chr2L 7000 8000 chr2R 27000 28000 1 + chr2L 7000 8000 chr2R 322000 323000 1 + chr2L 7000 8000 chr2R 397000 398000 1 + ...