diff --git a/docs/changelog.md b/docs/changelog.md index c6f9ad6e..0f7cfac0 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -1,7 +1,7 @@ # Change log All notable changes to this project will be documented in this file. -## [0.9.8] -- 2020-10-19 +## [0.9.8] -- 2020-10-22 ### Added - Add Q1 FRiP for improved cross protocol QC comparisons @@ -10,6 +10,8 @@ All notable changes to this project will be documented in this file. ### Changed - Update peak coverage table calculation to handle compressed files - Keep the non-normalized peak coverage table for some downstream analyses + - Enable the peak counts table to adjust the minimum number of samples a peak must be present in to be kept (`--cutoff`) + - Enable the peak count table to use raw read counts (default), weight the read count by the percentage overlap of the read in a peak (`--poverlap`), use the normalized read count (`--normalized`), or weight the normalized read count by the percentage overlap (`--poverlap --normalized`) ## [0.9.7] -- 2020-10-16 diff --git a/docs/usage.md b/docs/usage.md index 2e2190a2..564b9ef7 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -22,7 +22,7 @@ usage: pepatac.py [-h] [-R] [-N] [-D] [-F] [-T] [--silent] [--verbosity V] [--motif] [--sob] [--no-scale] [--prioritize] [--keep] [--noFIFO] [--lite] [--skipqc] [-V] -PEPATAC version 0.9.7 +PEPATAC version 0.9.8 optional arguments: -h, --help show this help message and exit diff --git a/usage.txt b/usage.txt index 33cea2cd..b42f2344 100644 --- a/usage.txt +++ b/usage.txt @@ -14,7 +14,7 @@ usage: pepatac.py [-h] [-R] [-N] [-D] [-F] [-T] [--silent] [--verbosity V] [--motif] [--sob] [--no-scale] [--prioritize] [--keep] [--noFIFO] [--lite] [--skipqc] [-V] -PEPATAC version 0.9.7 +PEPATAC version 0.9.8 optional arguments: -h, --help show this help message and exit