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Old 01-15-2013, 05:39 AM   #1
dragon0711
Junior Member
 
Location: germany

Join Date: Mar 2010
Posts: 1
Question bambus scaffolds on two mate pair libraries

Hi mira/bambus users,

we are running mira on hybrid libraries from 454 and illumina sequencers. To get nice scaffolds we are using bambus, which works quite well if we either use an illumina mate pair OR an 454 paired end data set. Now I tried the following .mate file for bambus:

Code:
library	illumina	100	1000	(HWUSI)*
pair	(.*)_.*\/1	(.*)_.*\/2
library	454large	3000	12000	([0-9A-Z]{14})*
pair	([0-9A-Z]{14})\.f	([0-9A-Z]{14})\.r
bambus (resp. detective) understood the names and what has to be forward and revers pair. goBambus resulted in:
Code:
  <LIBRARY ID="lib_illumina" NAME="illumina" MIN="100" MAX="1000">
    <INSERT ID="ins_2875100" NAME="HWUSI-EAS1580R:8:FC:6:61:6679:20212">
      <SEQUENCE ID="seq_1976804" NAME="HWUSI-EAS1580R:8:FC:6:61:6679:20212_1:N:0:CGTACTAG/1"/>
      <SEQUENCE ID="seq_1976805" NAME="HWUSI-EAS1580R:8:FC:6:61:6679:20212_2:N:0:CGTACTAG/2"/>
    </INSERT>
     <INSERT ID="ins_2875137" NAME="HSOHGH202BO3NA">
      <SEQUENCE ID="seq_1308766" NAME="HSOHGH202BO3NA.f"/>
      <SEQUENCE ID="seq_1306534" NAME="HSOHGH202BO3NA.r"/>
    </INSERT>
But the detective XML file contains only one library tag for the illumina library and all forward/reverse pair, the illumina AND the 454 reads, are grouped in this library. Is it possible to tell the programm to create an xml file which uses two libraries with two different insert sizes? If not, does anyone know an alternativ solution?

all the best

dragon0711

Last edited by dragon0711; 01-15-2013 at 06:50 AM.
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Old 11-16-2013, 08:10 PM   #2
norkish
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Location: Utah, USA

Join Date: Jun 2012
Posts: 1
Default Did you ever get an answer?

I have the same question. Did you find a resolution to this problem? Thx
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