[mira_talk] Re: 454 cleaning
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 5 Dec 2010 12:31:03 +0100
On Donnerstag 02 Dezember 2010 Robin Kramer wrote:
> Is their a particularly easy way to go about parsing ssaha2 files, or will
> the information be in the ACE file?
Hmmm ... the easiest way for you:
Start an assembly as you would do normally, but specify -CL:pec=no
Monitor the output, you will see
---------------------
Pass: 1
Performing snapshot 1
Localtime: Sun Dec 5 12:29:40 2010
Localtime: Sun Dec 5 12:29:40 2010
Making alignments
---------------------
Once this is there, kill the assembly (you don't need more). Look into the
checkpoint subdirectory. You will find there a MAF file. Use convert_project
to convert that back to FASTA where the clips have been removed:
convert_project -f maf -t clippedfasta input.maf output
Now use BLAST/SMALT/SSAHA2/FASTA3/whatever on that fasta file to search for
adaptor fragments which were not found.
B.
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