diff --git a/doc/protocols_pipelines.rst b/doc/protocols_pipelines.rst index ee095e4..7dcb2bc 100644 --- a/doc/protocols_pipelines.rst +++ b/doc/protocols_pipelines.rst @@ -56,16 +56,13 @@ Recommended pairtools parameters for standard Hi-C protocols To adapt the standard workflow for common variations of the Hi-C protocol, consider adjusting the following parameters: -1. `pairtools parse --walks-policy`: This parameter determines how pairtools parse handles reads with multiple alignments (walks). - We recommend specifying the value explicitly, as the default has changed between versions of `pairtools parse`. +1. ``pairtools parse --walks-policy``: + +This parameter determines how pairtools parse handles reads with multiple alignments (walks). We recommend specifying the value explicitly, as the default has changed between versions of ``pairtools parse``. - - Our current recommendation is to use `--walks-policy 5unique`, which is the default setting in the latest version of pairtools. - With this option, pairtools parse reports the two 5'-most unique alignments on each side of a paired read as a pair. - This option increases the number of reported pairs compared to the most conservative `--walks-policy mask`. - However, it's important to note that 5unique can potentially report pairs of non-directly ligated fragments - (i.e., two fragments separated by one or more other DNA fragments) as directly ligated. Such non-direct (also known as - "higher-order" or "nonadjacent") ligations have slightly different statistical properties than direct ligations, - as illustrated in several Pore-C papers [`1 `_ , `2 `_]. +Our current recommendation is to use ``--walks-policy 5unique``, which is the default setting in the latest version of pairtools. With this option, pairtools parse reports the two 5'-most unique alignments on each side of a paired read as a pair. + +This option increases the number of reported pairs compared to the most conservative ``--walks-policy mask``. However, it's important to note that ``5unique`` can potentially report pairs of non-directly ligated fragments (i.e., two fragments separated by one or more other DNA fragments). Such non-direct (also known as "higher-order" or "nonadjacent") ligations have slightly different statistical properties than direct ligations, as illustrated in several Pore-C papers [`1 `_ , `2 `_]. - An alternative is the `--walks-policy 3unique` policy, which reports the two 3'-most unique alignments on each side of a paired read as a pair, thus decreasing the chance of reporting non-direct ligations.