![]() ![]() When running Phred, make sure to create (a) a single FASTA file, (b) a single FASTA.QUAL file, and (c) SCF files.Ideally, use only letters, numbers, and underscores. Avoid using "funny" characters (like spaces, \, /, #.Before analyzing files with Phred, make sure all file names are less than 32 characters long.For the impatient, here are some guidelines to follow to avoid the common problems: User preferences for importing are set toĪ detailed description of these problems is given below.The sequence in trace files does not match the sequence in the FASTA files.Sequencher tries to open the wrong trace files ( Files are not where they should be).Long file names(especially on Windows when processing ABI 3700 data).Some of the most common reasons for these problems are: The sequences have wrong file names (like seq.fasta #1) and no qualities. ![]() The qualities shown in Sequencher do not make sense.You cannot open the chromatograms after importing.Importing does not import all the sequences in the fasta file.Sequencher does not show the qualities, or shows qualities only for some of the imported sequences.Sequencher gives an obscure error message when trying to import.Sequencher is a leading tool for contig editing and assembly developed by Gene Codes Corporation.Ī number of things can go wrong when trying to import qualities from a Phred-generated. For general instructions on importing Phred qualities into Sequencher, click here. This page describes some problems you may encounter when trying to import files with Phred qualities into Sequencher version 4. Sequencher Troubleshooting Sequencher Troubleshooting ![]()
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