Cogent NGS Analysis Pipeline notices
The issues described below for the Cogent NGS Analysis Pipeline are ones that have been seen or reported. If you encounter other errors using CogentAP or are unable to resolve the problem using the suggestions below, please:
- Capture a screenshot of the text of the error you see on the screen.
- Gather the relevant log file(s). Refer to the FAQ entry below for more detailed information about the logs.
- Send the screenshot and gathered log file(s) to Technical Support, along with a brief description of the issue.
Software issues FAQs
List & description of log files
| Problem area | Log filename | Directory location |
| Installation | CogentAP_install.log | %COGENT_AP_HOME |
| Demuxer | demux_demuxer.log | [Configured demux output folder] (see Figures 1 and 2) |
| Analyzer | analysis_analyzer.log | [Configured analysis output folder] (see Figures 1 and 3) |
Figure 1. Locations to find the demux and analysis output folders from the UI configuration.
Figure 2. Location to find the demux output folder from the command line.
Figure 3. Location to find the analysis output folder from the command line.
RNA-seq
Cogent NGS Analysis Pipeline
Analyze RNA-seq data generated by select Takara Bio applications.
Cogent NGS Discovery Software
Visualize RNA-seq data in UMAP or t-SNE charts from the output of the Cogent NGS Analysis Pipeline.
SMART-Seq DE3 Demultiplexer
Demultiplex sequencing data from SMART-Seq mRNA 3′ DE into sorted read data files.
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