Flow Documentation

Partek Flow Documentation

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In addition, the Post-alignment QA/QC report for single-end reads (Figure 1) contains the Unique column. That column contains This refers to the fraction of uniquely aligned reads.

 

Numbered figure captions
SubtitleTextPost-alignment QA/QC output table for single-end sequencing
AnchorNameresult-table

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On the other hand, the the Post-alignment QA/QC report report for paired-end reads (Figure 2) contains these columns:

  • Unique

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  • singleton 
    • fraction of alignments corresponding to the reads where only one of the paired reads can be uniquely aligned

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  • Unique paired 
    • fraction of alignments corresponding to the reads where both of the paired reads can be uniquely aligned

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Numbered figure captions
SubtitleTextPost-alignment QA/QC output table for single-end sequencing
AnchorNameresult-table

Image Removed

  • Non-unique singleton
    • fraction of singletons that align to multiple locations
  • Non-unique paired
    • fraction of paired reads that align to multiple locations

 

Numbered figure captions
SubtitleTextPost-alignment QA/QC output table for paired-end sequencing
AnchorNameresult-table-paired

Image Modified

In addition to the summary table, several graphs are plotted to give a comparison across multiple samples in the project. Those graphs are Alignment breakdown, Coverage, Average base quality per position, Average base quality score per read, and Average alignments per read. Two of those (Average base quality plots) have already been described.

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