[mira_talk] convert_project non-IUPAC
- From: "Sahl, Jason" <JSahl@xxxxxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 31 Oct 2012 19:52:56 +0000
Hello,
I am working with a 454 assembly done with v3.4. Now I'm trying to filter the
assembly with convert_project with this command:
convert_project -f caf -t fasta -r C -x 200 -y 5 K1461_out.caf K1461_caf_filter
I'm trying to force non-IUPAC bases with the "-r C" flag, but after filtering,
the IUPAC bases are still there. I have tried both the maf and caf files with
Mira 3.4 and 3.95. This is a non-hybrid assembly on a single isolate. I
should be able to force non-IUPAC consensus even if I didn't set that flag in
the manifest file, correct?
Thank you,
Jason
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