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ankitarathore 05-07-2013 11:26 PM

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

Pol8 10-12-2014 06:28 AM

Hi, I want to run a de novo with trinity. Which command should I use to start? I have single reads in fq

ezattara 10-13-2014 11:34 AM

You should check 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.

Nanu 10-17-2014 08:11 PM

If RAM is 1GB then what to do?

GenoMax 10-18-2014 04:05 AM


Originally Posted by Nanu (Post 152397)
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.

Nanu 10-28-2014 08:03 AM


I executed the fastqc , fastx and indexing the reference genome through Bowtie. When i executing the 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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