bambus scaffolds on two mate pair libraries

dragon0711 · 01-15-2013, 06:39 AM

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

norkish · 11-16-2013, 09:10 PM

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

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01-15-2013, 06:39 AM	#1
dragon0711 Junior Member Location: germany Join Date: Mar 2010 Posts: 1	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 07:50 AM.

11-16-2013, 09:10 PM	#2
norkish Junior Member Location: Utah, USA Join Date: Jun 2012 Posts: 1	Did you ever get an answer? I have the same question. Did you find a resolution to this problem? Thx