[mira_talk] Re: MIRA / large contigs
- From: Martin MOKREJŠ <mmokrejs@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 14 May 2014 22:07:19 +0200
Hi,
Bastien Chevreux wrote:
> On 13 May 2014, at 14:01 , Sabrina rodriguez
> <sabrina.rodriguez@xxxxxxxxxxxxxxxx> wrote:
>> In some cases, eventhough I obtain large contigs (> 500bp) as observed from
>> the <project>_info_assembly.txt file in the <project>_info directory; in the
>> <project>_result directory, no "LargeContigs" files were generated.
>
> Hello Sabrina,
>
> I base my answer on the assumption you are using a MIRA 4.x version. If not,
> please upgrade.
>
> There may be a couple of reasons for what you are seeing. Let’s go through:
>
> 1. A bug in MIRA. Possible, but I’d be a little bit surprised.
>
> 2. Is the “large contigs” info file in the info directory populated, that is,
> does it contain contig names. If yes, then “something” went wrong “somewhere”
> when MIRA, after the main assembly, called itself to extract the contigs.
> However, I think that this scenario is unlikely as you observe this only “for
> some cases / datasets”.
>
> 3. If the “large contigs” info file in the info directory is not populated,
> your data set is … weird, and fools the heuristics which determine what to
> consider as “large contig.” This heuristic works like this: during assembly,
> MIRA looks at all contigs >= 5kb to determine an average coverage of those
> contigs >= 5kb. Then, at the end of the assembly, it defines as “large”
> contigs all contigs >= 500bp which have a coverage being at least 50% of the
> previously calculated average coverage (33% on projects with a coverage <40x).
Um, for EST projects I would propose going for 2000 only. 5kb is too much. Did
you say 5kb is for genome assemblies only? ;-)
Can one decrease the 50% threshold (for EST projects ...)?
>
> BTW: you can change the 500 bp and 5000 bp limits via -MI:lcs and -MI:lcs4s
> parameters, maybe you want to test lcs=500 and lcs4s=2000. But please read on.
>
>> In one example, I have obtained contig lengths going from 120 bp to 4543.
>> In a second example, I have obtained contigs length between 107 and 9432 bp.
>
> So, in the first example I can totally understand why MIRA did not extract
> any contig as “large” contig: there was none >= 5 kbp to calculate statistics
> on, hence no average coverage estimation could be given. In the second
> example however I wonder a little bit what kind of other effect prevented at
> least the 9kbp contig to be regarded as large.
>
> However, in case you were not assembling some viral data, your assembly stats
> point to some deeper problem: projects with a max contig size of 9 kbp (let
> alone 4 kbp) are a total catastrophe. Something feels very wrong there.
Most likely bad adapter/primer/artifact removal. ;)
Martin
--
Martin Mokrejs, PhD.
454 / IonTorrent / Evrogen MINT / Clontech SMART adapter/artifact removal (...
too many protocols to name here)
http://www.bioinformatics.cz/software/supported-protocols/
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