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2. GS Reference Mapper : 2.17 GS Reference Mapper Output : 2.17.2 GS Reference Mapper cDNA / Transcriptome Output
2.17.2
GS Reference Mapper cDNA / Transcriptome Output
Output for cDNA / transcriptome mapping is found in the 454RefStatus.txt file (see Section 2.17.1.12) and the 454GeneStatus.txt file (below). There is also relevant information in the 454MappingQC.xls file (Section 2.17.1.11), but with certain differences described in Section 2.17.2.2.
 
2.17.2.1
454GeneStatus.txt
This gives statistical information regarding the number of reads that mapped exclusively to each gene. It has five fields:
 
1.
Gene Name – the name is the gene’s identifier in the related annotation database
2.
Num Unique Matching Reads – the number of reads mapping exclusively to one or more of the transcript variants for each gene. Note that reads mapping equally well to more than one transcript variant for a gene are still considered Repeats in terms of their final ReadStatus, but are included in this statistic if they only map to variants of a single gene.
3.
Pct of all unique matches – the number of reads exclusively mapped to the gene (as described above) divided by the total number of reads that mapped exclusively to any of the reference sequences
4.
Pct of All Reads – the number of reads exclusively mapped to the gene (as described above) divided by the total number of reads in this mapping project
5.
Description – the description obtained from the annotation data or renaming file
 
Figure 92: 454GeneStatus.txt file example
 
2.17.2.2
454MappingQC.xls
The following six columns present in the cumulative errors by base position table for Genomic mapping projects (see Section 2.17.1.11) do not appear when mapping cDNA reads to a cDNA reference: accno, position, Avg Unique Depth, Min Unique Depth, Max Unique Depth, and Depth Score. In their place, the following five columns are reported:
 
1.
Type – cDNA references are grouped into three categories: Short, Medium or Long. References less than 1500 base pairs long are categorized as “Short”. References greater than or equal to 1500 base pairs long but less than 3500 base pairs are categorized as “Medium”. References equal to or greater than 3500 base pairs are categorized as “Long”.
2.
Percent – this column is a histogram of averaged length percentiles for all cDNA references of a given Type
3.
Obs./Exp. Depth – number of reference bases within the percentile that were covered by reads, divided by the total number of reference bases in the percentile
4.
Avg. Depth – average of the number of reads mapping to each reference in the given length percentile
5.
MaxDepth – maximum number of reads mapping to a single reference in the given length percentile
 
Figure 93: 454MappingQC.xls file example for mapping to a cDNA reference