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:
bambus (resp. detective) understood the names and what has to be forward and revers pair. goBambus resulted in:
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
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
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>
all the best
dragon0711
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