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Old 05-08-2013, 12:26 AM   #1
ankitarathore
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Default De novo assembly using Trinity

After de novo assembly using Trinity, how to calculate coverage??

Last edited by ankitarathore; 05-21-2013 at 01:31 AM.
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Old 10-12-2014, 07:28 AM   #2
Pol8
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Hi, I want to run a de novo with trinity. Which command should I use to start? I have single reads in fq
thanks
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Old 10-13-2014, 12:34 PM   #3
ezattara
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You should check http://trinityrnaseq.sourceforge.net/ for details.

But something like the following should get you running:

Trinity --seqType fq --JM 100G --single reads.fq --CPU 6

Check your available RAM memory and number of cores to assign correctly the JM and CPU parameters. Substitute "reads.fq" for your read file.
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Old 10-17-2014, 09:11 PM   #4
Nanu
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If RAM is 1GB then what to do?
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Old 10-18-2014, 05:05 AM   #5
GenoMax
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Quote:
Originally Posted by Nanu View Post
If RAM is 1GB then what to do?
Not much (at least not in terms of de novo assembly). Unless the genome you are working on is the size of a small bacteriopahge.
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Old 10-28-2014, 09:03 AM   #6
Nanu
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Genomax,

I executed the fastqc , fastx and indexing the reference genome through Bowtie. When i executing the tophat2..it created the accepted.bam and unmapped.bam, align-summary.txt, logs etc...
Here I got only 1 KB size of accepted hits..while unmapped.bam is 200MB in size. i have heterologous reference genome. I downloaded the genome from Ensembl database. I have to find the novel gene, its expression.

Is any particular pipeline for roche transcriptome data?

I am trying to evaluate as denovo through trinity for roche transcriptome data analysis. here increased the RAM as 6GB.

Please help me..
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