[mira_talk] Re: 0.5TB not enough space?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Aug 2011 21:25:49 +0200
On Monday 15 August 2011 21:12:40 Iddo Friedberg wrote:
> Many repeats in Mycoplasma, unfortunately. Also, many HGTs, so k-mer
> frequencies may not be as uniform as in other bugs. But thanks for turning
> my attention to this, I will try running the assembly with some nasty
> repeat masking.
Nope, repeats are not your primary concern. The histogram is pretty healthy
regarding that ... I'd expect the usual rRNA repeats and maybe a couple of
highly repetitive short stretches which will probably break contig building at
a couple of places, but nothing really too wild I would say.
Run the first assembly n the reduced data set without repeat masking and
decide then on the resulting histogram and the repeat info file what to do
next.
> @Bastien "Heavens! Is there any valid reason you set up an assembly with a
> coverage >= 1000x?"
>
> Not one which I would like to put down in writing ;)
He he :-)
Fortunately the remedy is simple: "head -somenumber input.fastq >output.fastq"
will be your friend here.
B.
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