@@ -747,12 +747,13 @@ Stores various log and error files.
- ``*.log`` files from R scripts: Each log file is produced by the corresponding R script and contains debugging information as well as warnings and errors:
- ``1.produceConsensusPeaks.R.log``
- ``2.DiffPeaks.R.log``
- ``3.analyzeTF.{TF}.R.log`` for each TF ``{TF}``
- ``4.summary1.R.log``
- ``5.binningTF.{TF}.log`` for each TF ``{TF}``
- ``6.summaryFinal.R.log``
- ``checkParameterValidity.R.log``
- ``produceConsensusPeaks.R.log``
- ``diffPeaks.R.log``
- ``analyzeTF.{TF}.R.log`` for each TF ``{TF}``
- ``summary1.R.log``
- ``binningTF.{TF}.log`` for each TF ``{TF}``
- ``summaryFinal.R.log``
- ``*.log`` summary files: Summary logs for user convenience, produced at very end of the pipeline only. They should contain all errors and warnings from the pipeline run.
...
...
@@ -972,9 +973,9 @@ If an R script fails with a technical error such as ``caught segfault`` (a segme
Replace ``{outputFolder}`` by the folder you used for the analysis, and adjust the ``0.checkParameters`` part also accordingly. Essentially, you just have to provide the path to the corresponding file that is located in the ``LOGS_AND_BENCHMARKS`` subdirectly within the specified output directory.
Replace ``{outputFolder}`` by the folder you used for the analysis, and adjust the ``checkParameters`` part also accordingly. Essentially, you just have to provide the path to the corresponding file that is located in the ``LOGS_AND_BENCHMARKS`` subdirectly within the specified output directory.
@@ -31,20 +31,22 @@ We also put the paper on *bioRxiv*, please read all methodological details here:
Change log
============================
Version 1.1.1 (2018-08-01, coming soon)
Version 1.1.1 (2018-08-01)
- Documentation updates (referenced the bioRxiv paper, extended the section about errors)
- updated the information on how to load the snakemake object into the R workspace in the corresponding R scripts
- fixed a small bug that made the Volcano plot and the circular one appear to have switched sides.
- fixed a bug that made the labels in the Volcano plot switch sides (thanks to Jonas Ungerbeck)
- merged some diagnostic plots for the AR classification in the last step
- renamed R scripts and R log files to make them consistent with the cluster output and error files
Version 1.1 (2018-07-27)
- added a new parameter *dir_TFBS_sorted* in the config file to specify that the TFBS input files are already sorted, which saves some computation time by not resorting them
- added a new parameter ``dir_TFBS_sorted`` in the config file to specify that the TFBS input files are already sorted, which saves some computation time by not resorting them
- updated the TFBS files that are available via download (some files were not presorted correctly)
- added support for single-end BAM files. There is a new parameter *pairedEnd* in the config file that specifies whether reads are paired-end or not.
- restructured some of the permutation-related output files to save space and computation time. The rule *concatenateMotifsPerm* should now be much faster, and the TF-specific *...outputPerm.tsv.gz* files are now much smaller due to an improved column structure
- added support for single-end BAM files. There is a new parameter ``pairedEnd`` in the config file that specifies whether reads are paired-end or not.
- restructured some of the permutation-related output files to save space and computation time. The rule ``concatenateMotifsPerm`` should now be much faster, and the TF-specific ``...outputPerm.tsv.gz`` files are now much smaller due to an improved column structure
Version 1.0.1 (2018-07-25)
- fixed a bug in *2.DiffPeaks.R* that sometimes caused the step to fail, thanks to Jonas Ungerbeck for letting us know
- fixed a bug in *3.analyzeTF* for rare corner cases when *DESeq* fails
- fixed a bug in ``2.DiffPeaks.R`` that sometimes caused the step to fail, thanks to Jonas Ungerbeck for letting us know
- fixed a bug in ``3.analyzeTF`` for rare corner cases when *DESeq* fails
