Flow Documentation

Partek Flow Documentation

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Compatible reads with junction are reported in a separate block of columns in the transcripts spreadsheet (“junction RPKM”).

 

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SubtitleText Number of reads per transcript (rows) and sample (columns). “Transcripts” spreadsheet provides raw number of compatible reads as well as scaled number of reads (RPKM) for each sample. In addition, Partek® Genomics Suite™ gives the scaled number of reads for compatible junction reads and for incompatible reads. For definitions, please refer to the text
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Considering genes with multiple transcripts, a read can be both counted as compatible for some transcripts, as well as counted incompatible for other transcripts of the same gene (Figure 4). Please note that this concept holds for single-end reads as well.

 

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SubtitleTextCompatibility of reads corresponding to genes with multiple transcripts. First in pair maps to all three transcripts, while second maps to transcripts A and B. The paired-end read is compatible with transcripts A and B, but is not compatible with the transcript C. Although the picture shows paired-end reads, the same rules apply for single-end reads
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With respect to the gene-level summarization, user can decide whether or not to consider intronic reads (both single- and paired-end) as compatible with the gene (Figure 5). In the latter case, the entire gene is basically treated as one giant exon. In the case that one end of a paired-end read falls within a gene, and the other end does not, the read will not be included in the gene-level summarization.

 

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SubtitleTextConfiguring the mRNA quantification. Gene-level result can report intronic reads as compatible or incompatible with genes. The option applies to both single-end and paired-end reads
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When interpreting the unexplained reads, you should have in mind that these are actually the reads not compatible with the applied transcript model. By changing the model, some reads will become compatible and thus will not be labeled “unexplained” any more. Figure 6 shows such an example. The depicted regions map just downstream of the human LONP2 gene as defined by RefSeq and are hence flagged as unexplained. However, by overlaying the AceView transcripts, it is apparent that mapping to AceView would yield a different result.

 

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SubtitleText Regions track in the Partek Genome Viewer. Regions (colored boxes) detected in the four samples contain sequencing reads that are not compatible with the RefSeq database (upper transcripts track) but are compatible with at least one of the exons of the same gene defined by the AceView database (lower transcripts track)
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