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Old 06-12-2011, 12:43 PM   #1
raw937
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Default MIRA assembly with MID barcodes for 454?

Does anyone know how to do use MIRA with a barcoding check prior to assembly???
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Old 06-14-2011, 02:09 PM   #2
maubp
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The easiest way is to use the (Linux only) Roche 454 off instrument applications to divide the SFF file by MID, then follow the normal MIRA approach.
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Old 06-14-2011, 06:06 PM   #3
raw937
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Default It asks for the trace files?

Hello,
It asks for the trace files (flowgrams), which you can omit with the command

mira --project=... --job=... --notraceinfo ...other parameters... according to Bastien Chevreux

but are the flowgrams useful? Because I want to directly compare MIRA to Newbler...Or are the qual files enough?
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Old 06-14-2011, 11:48 PM   #4
maubp
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Are you talking about the XML clipping file from sff_extract? You can get that by running sff_extract on the MID filtered SFF file (i.e. follow the normal MIRA approach).
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Old 06-14-2011, 11:54 PM   #5
sklages
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Quote:
Originally Posted by raw937 View Post
Hello,
It asks for the trace files (flowgrams), which you can omit with the command

mira --project=... --job=... --notraceinfo ...other parameters... according to Bastien Chevreux

but are the flowgrams useful? Because I want to directly compare MIRA to Newbler...Or are the qual files enough?
'traceinfo' is just some clipping information provided as XML to MIRA.
See http://mira-assembler.sourceforge.ne..._xml_traceinfo

As maubp has already mentioned, you need to split your SFF files according to the MIDs used before you can use MIRA (.e.g. using Roche's sfftools).
Then you can either use Roche's sfftools or sff_extract to generate MIRA compliant FASTA input files.

hth, Sven
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