De novo assembly using Trinity

[ankitarathore]

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

[Pol8]

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

[ezattara]

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.

[Nanu]

If RAM is 1GB then what to do?

[GenoMax]

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]

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..