Cogent NGS Analysis Pipeline notices
The issues described below for the Cogent NGS Analysis Profiler 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.
Data analysis FAQs
Columns in Stats file
The tables below document all potential columns that might display in a Cogent NGS Analysis Pipeline Stats file; they also represent the column names accepted for input into Cogent NGS Discovery Software.
Columns that will be present in all Stats files output by CogentAP (input workflow agnostic).
Column name | Description |
---|---|
Barcode | Detected barcodes. This value will usually be the sample name from the well-list or well-list-like file, but there are three exceptions, documented in the table below. |
Sample | Sample names described in sample description file. |
Barcoded_Reads | Number of reads after demultiplexing. |
Trimmed_Reads | Number of remained reads after trimming. |
Unmapped_Reads | Number of reads not mapped to genome. |
Mapped_Reads | Number of reads mapped to genome. |
Multimapped_Reads | Number of reads mapped to multiple genomic locations. |
Uniquely_Mapped_Reads | Number of reads mapped to one genomic location. These reads are used for counting. |
Exon_Reads | Number of reads assigned to an exonic region. |
Ambiguous_Exon_Reads | Number of reads assigned to exonic regions of multiple genes. |
Intron_Reads | Number of reads assigned to an intronic region. |
Ambiguous_Intron_Reads | Number of reads assigned to intronic regions of multiple genes. |
Gene_Reads | Number of reads assigned to a gene region (exon + intron). |
Intergenic_Reads | Number of reads assigned to an intergenic region. |
No_of_Genes | Number of detected genes. |
Mitochondrial_Reads | Number of reads assigned to mitochondrial chromosome. |
Ribosomal_Reads | Number of reads assigned to a ribosomal gene. |
The "Barcode" column, in addition to the samples named in the well-list or well-list-like file, will also have three additional rows, which are described in the following table.
Barcode field value | Description |
---|---|
Short | Number of reads containing N in barcode or having shorter length than barcode. |
Unselected | Number of reads having a barcode included in Chip’s description, but not included in sample description file. |
Undetermined | Number of reads having undetermined barcode. |
Additional columns in the Stats file for 3′ DE analysis with UMIs on ICELL8 system.
The table below lists additional columns that will be present in the Stats file when the input FASTQ files result from the ICELL8 3′ DE for UMI Reagent Kit (Cat # 640005) workflow on the ICELL8 Single-Cell System (Cat # 640000).
Column name | Description |
No_of_UMIs | Number of UMI variations detected after demultiplexing. |
Exon_nUMIs | Number of deduplicated reads assigned to an exonic region. Deduplication is done by UMI. |
Intron_nUMIs | Number of deduplicated reads assigned to an intronic region. Deduplication is done by UMI. |
Gene_nUMIs | Number of deduplicated reads assigned to a gene region (exon + intron). Deduplication is done by UMI. |
Additional columns in Stats file for the SMARTer Stranded Total RNA-Seq Kit v3- Pico Input Mammalian protocol.
The table below lists additional columns that will be present in the Stats file when the input FASTQ files result from the SMARTer Stranded Total RNA-Seq Kit v3- Pico Input Mammalian protocol.
Column name | Description |
No_of_UMIs | Number of UMI variations detected after demultiplexing. |
Exon_nUMIs | Number of deduplicated reads assigned to an exonic region. Deduplication is done by UMI. |
Exon_nUSSs | Number of deduplicated reads assigned to an exonic region. Deduplication is done by Unique Start&Stop Site (USS). |
Exon_nUMIs_USSs | Number of deduplicated reads assigned to an exonic region. Deduplication is done by both UMI and USS. |
Intron_nUMIs | Number of deduplicated reads assigned to an intronic region. Deduplication is done by UMI. |
Intron_nUSSs | Number of deduplicated reads assigned to an intronic region. Deduplication is done by Unique Start&Stop Site (USS). |
Intron_nUMIs_USSs | Number of deduplicated reads assigned to an intronic region. Deduplication is done by both UMI and USS. |
Gene_nUMIs | Number of deduplicated reads assigned to a gene region (exon + intron). Deduplication is done by UMI. |
Gene_nUSSs | Number of deduplicated reads assigned to a gene region (exon + intron). Deduplication is done by Unique Start&Stop Site (USS). |
Gene_nUMIs_USSs | Number of deduplicated reads assigned to a gene region (exon + intron). Deduplication is done by both UMI and USS. |
Strand_Specificity | Ratio of reads detected as correct strand after mapping to genome. |
RNA-seq
Cogent NGS Analysis Pipeline
Analyze RNA-seq data generated from ICELL8 system 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 the SMART-Seq v4 3′ DE Kit into sorted read data files.
Takara Bio USA, Inc.
United States/Canada: +1.800.662.2566 • Asia Pacific: +1.650.919.7300 • Europe: +33.(0)1.3904.6880 • Japan: +81.(0)77.565.6999
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES. © 2020 Takara Bio Inc. All Rights Reserved. All trademarks are the property of Takara Bio Inc. or its affiliate(s) in the U.S. and/or other countries or their respective owners. Certain trademarks may not be registered in all jurisdictions. Additional product, intellectual property, and restricted use information is available at takarabio.com.