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Old 10-09-2014, 09:37 AM   #1
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Default on MIRA with fasta input


I have a fasta file, and I want to run a de novo on MIRA. How can I tell the program that it's not a fastq file and run it?
Pol8 is offline   Reply With Quote
Old 10-09-2014, 10:07 AM   #2
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MIRA automatically recognises what type the sequence data is by looking at the postfix of files. For postfixes not adhering widely used naming schemes for file types, there's additionally a way of explicitly defining the type (see further down at the end of this item on how this is done). Currently allowed file types are:

.fasta for sequences formatted in FASTA format where there exists an additional .fasta.qual file which contains quality data. If the file with quality data is missing, this is interpreted as error and MIRA will abort.

.fna and .fa also for sequences formatted in FASTA format. The difference to .fasta lies in the way MIRA treats a missing quality file (called .fna.qual or .fa.qual): it does not see that as critical error and continues.
You would want to name your files *.fa if you do not have corresponding qual files.
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Old 10-09-2014, 01:45 PM   #3
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You also, unless you really know what you are doing, should consider not using sequence reads without quality data with Mira, unless you have chopped up a finished sequence and are doing something with that.
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