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... andrejhaven't used MGRAST but I presume you need fastq, python stript from QIIME should do that from fasta and qual fileshttp://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:HiiI 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
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