Trimming is one of several Project Report views and is only available for de novo assemblies of Sanger trace data. When present, the report provides information about quality trimming and vector removal done as part of the SeqMan NGen assembly.
To access the view, choose View > Project Report > Trimming.
The Trimming report lists the name of each sequence, its average quality, amount trimmed, and the trimmed and pre-trimmed lengths.
|Located above the table|
|Trace Threshold||The maximum value of the trace score associated with each base. This is used for end trimming of low quality bases.|
|Qual Threshold||The maximum value of the quality score associated with each base. This is used for end trimming of low quality bases.|
|Located in the table|
|Non-Trace Window Size and Max Ns||SeqMan NGen trims data from sequence ends based on the number of ambiguous residues (Ns) within each sliding window. If the first number was 50 and the second number was 2, for example, this would show that SeqMan NGen trimmed sequence ends to leave two or fewer ambiguous bases (Ns) in the first and last 50 bases in the sequence.|
|Name||Name of the read file followed by parentheses showing the position of the sequence on the consensus.|
|Average Quality||The average quality of bases that remained after trimming this sequence.|
|Amount Trimmed||Number of bases removed from the sequence, in base pairs.|
|Trimmed Length||The final length of this sequence after trimming.|
|Pre-Trimmed Length||The original length of this sequence prior to trimming.|
To export data from this view, press the Export data tool ( ) in the top right of the view. This opens a save dialog in which you can save the tabular data in comma-separated (.csv) or tab-separated (.tab) format.
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