[mira_talk] HAF tag recovery
- From: Remi Moulinas <remi.moulinas@xxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 21 Nov 2013 15:48:22 +0100
Hello,
Following the advice you gave in a previous topic
On 10/15/2013, Bastien Chevreux wrote:
to see how you can change the boundaries. E.g., you can redefine
HAF5 to be set only for repeats >=10x, HAF6 for >=20x, HAF7 >=50x
and MNRr for >=200x.
In short: MIRA can give you a list of reads with the sequence
stretches which fall into the different repeat level categories MIRA
has.
To get this data without doing a full assembly, use the parameter -AS:nop=0
I am trying to recover in the *_info_readrepeats.lst the full list of
HAF tag using this paramaters :
project = C2_coverage_nop
job = genome,denovo,accurate
parameters = -GE:not=8 \
-AS:nop=0 \
-HS:rliif=2:fenn=1:fexn=2:fer=5:fehr=10:fecr=20:mnr=yes:nrc=0:nrr=100:ldn=no
Those parameters are correctly interpreted as I can see them in the log file :
Parameters for Hash Statistics (-HS):
Freq. cov. estim. min (fcem) : 0
Freq. estim. min normal (fenn) : 1
Freq. estim. max normal (fexn) : 2
Freq. estim. repeat (fer) : 5
Freq. estim. heavy repeat (fehr) : 10
Freq. estim. crazy (fecr) : 20
Mask nasty repeats (mnr) : yes
Nasty repeat ratio (nrr) : 100
Nasty repeat coverage (nrc) : 0
Lossless digital normalisation (ldn) : no
Repeat level in info file (rliif) : 2
but in the *_info_readrepeats.lst file, I can only see HAF tag from
HAF5 to MNRr.
Even in modifying the parameters (with same input) :
-HS:rliif=2:fenn=5:fexn=10:fer=15:fehr=20:fecr=30:mnr=yes:nrc=0:nrr=100:ldn=no
I still can't see HAF2-HAF3...In the doc it is true that rliif is 0 or
5-8 so is there a way to recover HAF2, HAF3 and HAF4 tag ?
Thank you for your suggestions and help
--
Rémi Moulinas
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