[mira_talk] Re: Illumina/Solexa sequence coverage.
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 15 Sep 2011 14:46:12 -0400
On 2011-09-15, at 12:52 PM, John Nash wrote:
> On 2011-09-14, at 2:59 PM, Bastien Chevreux wrote:
>
>> On Sep 13, 2011, at 23:27 , John Nash wrote:
>>> I guess that I am asking what the command line parameters are to take a CAF
>>> file from a hybrid assembly and then use it as input for a mapping assembly
>>> against a reference genome. Or should I dump the contigs as fastq files
>>> and use those.
>>
>> What you're looking for is
>> -SB:bft=caf
>>
>> Also have a look at the othe -SB parameters ... you especially want to
>> assign a strain to the CAF sequences and another one to the sequences of
>> your other bug.
>
> Sorry, I should have been more explicit...
>
> Since the CAF file is a mixture of data from a hybrid assembly, do I call it
> sanger, 454 or solexa (or all 3) when passing the
> "--project=mapping,genome,accurate,xxx "parameters to mira
To answer my own question... I lied to mira.
nohup mira --project=PROJ --job=mapping,genome,accurate,sanger
--caf=PROJ_in.sanger.caf COMMON_SETTINGS -GE:kpmf=15:not=40 -MI:somrnl=0
-SB:bft=gbf:abnc=yes >&PROJ_log_assembly.txt &
And she believed me:
Backbones: 1 Backbone rails: 3678
Sanger 454 IonTor PacBio Solexa SOLiD
----------------------------------------
Total reads 0 477157 0 0 5401329 0
Reads wo qual 0 0 0 0 0 0
Used reads 0 477157 0 0 5401323 0
Avg tot rlen 0 518 0 0 75 0
Avg rlen used 0 456 0 0 68 0
With strain 0 0 0 0 0 0
W/o clips 0 20311 0 0 3497171 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:247612459 used bases in used reads: 218033668
IonTor total bases:0 used bases in used reads: 0
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:410479546 used bases in used reads: 367900491
Solid total bases:0 used bases in used reads: 0
Bastien, you are a genius.
John
Other related posts:
