[mira_talk] Several illumina insert sizes
- From: Nestor Zaburannyi <nestor@xxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 12 Jul 2011 15:41:57 +0200
Dear all.
I have come to a point in which i must use several illumina libraries with
various insert sizes for assembly. However, even after generating *.xml for
only one of them, i got 1300MB file. Mira doesn't like this volume of xml i
guess, because it takes all the RAM and all the SWAP space and doesn't progress
any further in observable future.
My only idea is to assemble one library and then use the contigs as false reads
with quality information. Or to assemble without any paired information at all.
Has anybody encountered such problems? Also, is my *.xml correct?
<?xml version="1.0"?>
<TRACE_VOLUME>
<TRACE>
<TI>1:4:1:1426:1923#ATGTAA/1</TI>
<TEMPLATE_ID>1:4:1:1426:1923#ATGTAA</TEMPLATE_ID>
<INSERT_SIZE>300</INSERT_SIZE>
<INSERT_STDEV>30</INSERT_STDEV>
<TRACE_END>FORWARD</TRACE_END>
</TRACE>
<TRACE>
<TI>1:4:1:1426:1923#ATGTAA/2</TI>
<TEMPLATE_ID>1:4:1:1426:1923#ATGTAA</TEMPLATE_ID>
<INSERT_SIZE>300</INSERT_SIZE>
<INSERT_STDEV>30</INSERT_STDEV>
<TRACE_END>REVERSE</TRACE_END>
</TRACE>
...
Sincerely yours
Nestor
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