[mira_talk] PROJ_default.(un)padded.fasta vs PROJ_ReferenceStrain vs PROJ_AllStrains
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 17 Oct 2011 13:27:44 -0400
Good afternoon,
I just did a mapping assembly of the results of a de novo assembly. It's an E.
coli strain with 40x 454 and 70X Illumina. After I did the de novo assembly, I
mapped it against K12 and now I am going to BLAST the non-K12 contigs to see
what I have.
I took the caf file and did:
$ convert_project -f caf -t fasta -t caf -x 500 -y 30 PROJ_out.caf
PROJ_out_LargeContigs
When I look at the results (ls -1 *.unpadded.fasta) so as not to list the
padded results and the qual files, I get:
PROJ_LargeContigs_AllStrains.unpadded.fasta
PROJ_LargeContigs_ReferenceStrain.unpadded.fasta
PROJ_LargeContigs_default.unpadded.fasta
I understand what the ReferenceStrain is - one contig was a HUGE hint :)
I also know that the other two files have a mapping to the backbone strain as
an entry. What else is different between them.
(I did do a Google search and read the manual, promise).
Thanks
John
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