@@ -53,9 +53,11 @@ We also put the paper on *bioRxiv*, please read all methodological details here:
...
@@ -53,9 +53,11 @@ We also put the paper on *bioRxiv*, please read all methodological details here:
Change log
Change log
============================
============================
Version 1.3 (2019-07-17)
Version 1.3 and 1.3.1 (2019-07-17)
- Various minor changes and small bug fixes as reported by users
- Various minor changes and small bug fixes as reported by users
- improved the RNA-Seq classification, further information will follow soon.
- improved the RNA-Seq classification, further information will follow soon.
- updated Documentation for errors that users reported and why they occur
- improved error messages in the pipeline for various cases
Version 1.2.5 (2019-03-13)
Version 1.2.5 (2019-03-13)
- Updated the TFBS_hg38_FIMO_HOCOMOCOv11 archive one more time to exclude non-assembled contigs such as HLA*. To make the pipeline more stable for such edge cases, the parameter ``dir_TFBS_sorted`` has been removed, and sorting and filtering of chromosomes is now always performed. Only chromosomes are kept in both the consensus peak files and the TFBS bed files that start with ``chr`` and are neither sex chromosomes (``chrX`` or ``chrY``) nor ``chrM``. If you want to keep sex chromosomes in your analysis (although we think this is not recommended), simply edit the Snakefile and remove the "chrX" and "chrY" occurences in the two filtering rules.
- Updated the TFBS_hg38_FIMO_HOCOMOCOv11 archive one more time to exclude non-assembled contigs such as HLA*. To make the pipeline more stable for such edge cases, the parameter ``dir_TFBS_sorted`` has been removed, and sorting and filtering of chromosomes is now always performed. Only chromosomes are kept in both the consensus peak files and the TFBS bed files that start with ``chr`` and are neither sex chromosomes (``chrX`` or ``chrY``) nor ``chrM``. If you want to keep sex chromosomes in your analysis (although we think this is not recommended), simply edit the Snakefile and remove the "chrX" and "chrY" occurences in the two filtering rules.
