[mira_talk] Parameters to assemble a microbial metatranscriptome

From: Alexis Blanchet-Cohen <alexis.blanchet-cohen@xxxxxxxxxxxxxx>
To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
Date: Mon, 23 Apr 2012 15:14:49 +0000

Hi,


I would like some advice on setting the parameters for assembling de novo a 
microbial metatranscriptome.


An sample was taken from the environment.

All the RNA (rRNA, tRNA, mRNA, ...) was extracted and reverse transcribed to 
cDNA.

The cDNA was sent for Solexa sequencing.


I have 240 000 paired end reads of 101 bases each.


I have no means of knowing the minimum and maximum lengths of the cDNAs or the 
average length.


How I set the tismin and tismax parameters?

There is no fixed insert size.


Here was my latest attempt. The values for tismin and tismax were set 
arbitrarily (Ok, they were copied from the example in the manual. :))


mira --project=arctic --job=denovo,genome,accurate,solexa SOLEXA_SETTINGS 
-GE:tismin=250:tismax=750


Thank you for your help,


Alexis

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[mira_talk] Parameters to assemble a microbial metatranscriptome

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