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Old 10-12-2014, 07:31 AM   #1
Pol8
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Location: USA

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Default Trinity - de novo: how to start

I want to run Trinity to check what assembly I get de novo. I know I have to get something from my reads (I previously used other programs). Which command should I use to see if I get something? I've tryed but do not get anything. I have single reads in fq.
thanks
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Old 10-12-2014, 03:32 PM   #2
ilovefungi
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first install trinity.

run trinity.pl, you will see the instructions how to use it. generally the command lines goes like:

trinity.pl --seqType xx --JM xx reads.fq --CPU x --output xx

if paired ends, you need to specify right end and left end, such as --right xx.fq --left xx.fq
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