[mira_talk] Re: FASTA WITH QUALITY VALUES
- From: Chayan Roy <chayan.roy93@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 26 Feb 2014 00:10:00 +0530
thanks to all of you for your kind helps.... okk so as per my requirement
if i use
$miraconvert -x 1000 -f fasta file.unpadded.fasta file .unpadded.fasta.qual
-t fastq
it should solve my purpose...i will give it a try obviouly...
thanks again
best
On Tue, Feb 25, 2014 at 8:51 PM, Veljo Kisand <vkisand@xxxxxx> wrote:
> you are correct, I was just fooled by description where it is not
> specifically mentioned
> Options:
> -f <fromtype> load this type of project files, where fromtype is:
> caf a complete assembly or single sequences from CAF
> maf a complete assembly or single sequences from CAF
> fasta sequences from a FASTA file
> fastq sequences from a FASTQ file
> gbf sequences from a GBF file
> phd sequences from a PHD file
> fofnexp sequences in EXP files from file of filenames
>
> specifying
> -f fasta file.fasta file.qual -t fastq
>
> works fine
>
> Veljo
>
>
>
> On 02/25/2014 05:20 PM, Andrej Benjak wrote:
>
>> why QIIME? miraconvert can produce fastq files...
>>
>> andrej
>>
>>> haven't used MGRAST but I presume you need fastq, python stript from
>>> QIIME should do that from fasta and qual files
>>> http://qiime.org/scripts/convert_fastaqual_fastq.html
>>>
>>> Veljo
>>>
>>> On 02/25/2014 04:03 PM, Lionel Guy wrote:
>>>
>>>> Yes.
>>>> >From the manual (http://mira-assembler.sourceforge.net/docs/
>>>> DefinitiveGuideToMIRA.html#sect_res_resultsdir):
>>>>
>>>> The *_d_results directory [...]
>>>>
>>>> * projectname_out.unpadded.fasta: as above, this file contains as
>>>> FASTA sequence the consensus of the contigs that were assembled in the
>>>> process, put positions in the consensus containing gaps were removed. The
>>>> computed consensus qualities are in the corresponding
>>>> projectname_out.unpadded.fasta.qual file.
>>>>
>>>> Lionel
>>>>
>>>> On 25 Feb 2014, at 14:58 , Chayan Roy <chayan.roy93@xxxxxxxxx> wrote:
>>>>
>>>> Hii
>>>>>
>>>>> I have performed an assembly on deep sequenced metagenome. Now i want
>>>>> to extract contigs larger than 1000. If i have to submit them in MGRAST i
>>>>> also need the quality values. I am not sure how to do this. I went through
>>>>> the manual and know how to use the convert_project to extract contigs
>>>>> >1000
>>>>> but dont know how add quality values on them. Will
>>>>> file.unpadded.fasta.qual
>>>>> will serve my purpose??
>>>>> Any help..
>>>>>
>>>>> Mira version: MIRA V3.4.0.1 (production version).
>>>>>
>>>>> Best
>>>>> --
>>>>> CHAYAN ROY
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>>
>
> --
> You have received this mail because you are subscribed to the mira_talk
> mailing list. For information on how to subscribe or unsubscribe, please
> visit http://www.chevreux.org/mira_mailinglists.html
>
--
*CHAYAN ROY*
Other related posts:
