[mira_talk] Re: Assembly genome pine

Bastien Chevreux escribió:
Ummm ... why are you setting a minimum read length of "3" for Sanger reads if you do only a 454 assembly? Did you forget the "454_SETTINGS" in front of -AS:mrl? And 3 is really really really a bit small.
Thank you for the sugerencia. You have reason, use-AS:mrl=3 has been one of the multiple tests that I have realized. For the case explaining to you a bit more, I am ensamblando genomic sequences and pine contained in vectors BAC, sequenced with 454. One of the principal characteristics of these sequences is that they possess 70 % of highly repetitive DNA. I have obtained the best results using: 

"mira -fasta -project=40B10 -job=denovo,genome,normal,454
-highlyrepetitive -LR:mxti=yes -FN:xtii=40B10_traceinfo_in.454.xml"
If you have really nasty repeats, try "-SK:mnr=yes", but be aware that this might mask away quite a bunch of data (adjustable via "-SK:rt"). 

I am going to try to change the parameter that you suggest me.

Thank you very much for everythinng.


Regards,

Rocío Bautista

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Rocío Bautista Moreno
Centro de Supercomputación y Bioinformática
Universidad de Málaga

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                                   29590 Málaga (SPAIN)




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