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After de novo assembly using Trinity, how to calculate coverage??
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Last edited by ankitarathore; 05-21-2013, 12:31 AM. -
Hi, I want to run a de novo with trinity. Which command should I use to start? I have single reads in fq
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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.Comment
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If RAM is 1GB then what to do?Comment
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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.Originally posted by Nanu View PostComment
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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..Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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