Note: This topic is not applicable to BAM-based projects.
End Trimming parameters determine how SeqMan Pro trims poor quality data from the ends of sequences. End trimming can be based on quality scores or by fixed endpoints.
Note: In addition to setting end trimming parameters, as described below, you must activate end trimming by selecting Trim sequence ends from the Preassembly and Assembly Options dialog.
Trimming parameters can be adjusted from the Unassembled Sequences window, by clicking the Trim Ends button or, by going to Project > Parameters and selecting End Trimming from the left side of the screen, as shown in the image.
•Quality Stringency is the best choice if you are using data from an automated sequencer or if your sequence runs vary in length. To trim based on quality, select Quality Stringency, then choose Low (corresponding to an averaged quality score threshold of 8) Medium (12) or High (16); or choose Other to specify quality Thresholds (0-100) for trace sequences, .fas files with .qual file scores, and .sff files, as well as set parameters for trimming non-trace sequences based on ambiguous residues.
o Trace Sequences - SeqMan Pro trims based on the shape and intensity of peaks.
o Qual File Scores - For .sff files, SeqMan Pro uses the quality scores within the .sff file for trimming. For .fas files, SeqMan Pro automatically checks for .qual files with the same name in the same folder. If found, the quality values are read from the .qual file into the project and SeqMan Pro uses these values for trimming. These .qual files may come from SeqMan Pro or Phred, among other sources.
o Non-Trace Sequences - SeqMan Pro trims data from the ends based on the number of ambiguous residues (Ns) within each sliding window. Example: If you set Window Size to 70 and Max(imum) Ns to 2, SeqMan Pro trims bases such that there are two or fewer Ns in the first and last 70 bases.
•Fixed End Points is the recommended choice if your data are of a set length and do not have any quality or confidence measurements. To use this method, select Fixed End Points and then type the 5’ End and 3’ End coordinates in the parameter box. SeqMan Pro will trim residues outside the boundaries you specify. To restore trimmed bases, type the word LEND into the 5’ End field and/or REND into the 3’ End field.
If you accessed end trimming parameters via the Trim Ends button in the Unassembled Sequences window, finish by choosing one of the following options:
•Click Scan Selections to trim ends now from selected sequences only.
•Click Scan All to trim the ends of all sequences.
•Click Scan Later to postpone end trimming until clicking the Assemble button.