Quality and MID trimming

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Quality and MID trimming

Postby BOM86 » Wed Mar 20, 2013 9:03 am

I have a problem when importing Roche-454 sequences into codoncode.
Since the new update it automatically trims of the MID and also automatically trims the sequences untill a certain PHRED score is achieved.
Is there a way to load in the sequences without the automated trimming?
BOM86
 
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Re: Quality and MID trimming

Postby Peter Richterich » Thu Mar 21, 2013 8:52 am

When importing 454 data from SFF files, the trimming information that is present in the SFF files will be applied; no other trimming is done automatically. To import untrimmed data, you could import from FASTQ format files instead; however, you will need to make sure that the 454 software you use to generate the FASTQ files writes untrimmed data.
Peter Richterich
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