[mira_talk] Re: Ignoring indels
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 10 Mar 2012 17:27:50 +0100
On 03/07/2012 07:29 PM, Jackie Lighten wrote:
Can I tell Mira to ignore indels, during my 454 /de novo/ EST accurate
assembly?
Could you please specify what you mean exactly by "ignoring indels".
MIRA is already very, very cautious when it comes to indels and 454
sequences ... it treats them like hot potatos.
Though you may want to play with with the -AL:egp* and -CO:amgb* settings.
Additionally, if this option exists can I ask mira to ignore indels
associated with a homopolymer run of a specified length?
Whatever you mean with "ignoring indels", there is no user tunable
parameter for length of indels and length of homopolymers.
If this is not possible can anyone recommend a simple solution to
batch remove indels from all contigs?
I'm slightly confused here ... what do you want to remove from where
exactly?
B.
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