Change log

All notable changes to this project will be documented in this file.

[0.4.0] -- 2017-07-21

Added

Added fseq as a peak caller option
Peak caller is specified by a command line argument (defaults to macs2)
Count of called peaks is now reported as a pipeline result.
Add R and ggplot2 as requirements

Changed

Changed TSS plotting to use R instead of python
TSS plot failures no longer fail the pipeline.
Changed Read_type to read_type to prevent duplicate columns
Read trimmer is now specified in option + argument style rather than as a flag.

[0.3.0] -- 2017-06-22

Added

Added exact cuts calculation
Added command-line version display
Added skewer as a trimmer option
Uses looper 'implied columns' (from looper v0.6) to derive multiple variables from organism value

Changed

Generalizes decoy alignments to pre-alignments, with a new --prealignment option
Simplified unmapped read processing to be output by bowtie directly, improving efficiency
Fixed bug that hard-coded mouse genome size in for macs, and fixed pipeline interface
Updated to new looper pipeline interface format
Pipeline now requires looper v0.6 or greater
Improved README

[0.2.0] -- 2017-04-17

Added

FRiP can now be calculated based on reference peaks
Pipeline now reports Picard estimated library size statistic
Added option for pyadapt trimming
Added example project using 'gold standard' data
Added new resource package grades
Added preliminary 'exact cuts' scripts, but they are not yet used

Changed

Improved README
Changed filename of the TSS file
Reorganized structure of alignment code

[0.1.0]

Added

First release of ATAC-seq pypiper pipeline