[mira_talk] Extracting contigs from mapped assembly / convert_project output
- From: Surya Saha <ss2489@xxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 27 May 2013 14:31:08 -0400
Hi Bastien and others,
I did a mapped assembly using the following parameters with MIRA 3.4.0 a
long time ago
--job=mapping,genome,accurate,solexa --noclipping COMMON_SETTINGS
-SB:load_backbone=on:startbackboneusage_inpass=1:backbone_filetype=fasta:abnc=on
-MI:stop_on_nfs=no:somrnl=0 SOLEXA_SETTINGS -LR:file_type=fastq
I am now trying to get the mapped contigs of my strain(excluding the
backbone) from the maf file using the following command (
//www.freelists.org/post/mira_talk/Denovo-versus-mappings-assembly-with-Mira,1
).
convert_project -f maf -t fasta mira_out.maf mynewresults
I get the following unpadded files -
XXX_default.unpadded.fasta
XXX_StrainX.unpadded.fasta
XXX_ReferenceStrain.unpadded.fasta
XXX_AllStrains.unpadded.fasta
I can figure out that ReferenceStrain is the backbone. What is the
difference between the three other files? They have very similar
characteristics. Thanks
Best,
Surya
-----------------------------------------------------
Surya Saha
Department of Plant Pathology
and Plant-Microbe Biology
Cornell University, NY, USA
http://www.linkedin.com/in/suryasaha
Twitter: @SahaSurya
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