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* What's about "align_to_scf" ?
This is important if you want to see the real traces within the contig editor from STADEN at a given position.
Note: there are no information given within the ACE assembly to recalculate the trace position backward from assembly.
STADEN "trev" will access/open traces as given from "sequencer machine" and Roche assembly give you only the complete assembly
information. This is the problem !
Are you firm with gap4 ?
The program "trev" is automatically called within "gap4".
And you start this with:
-> open gap4 database
--> open contig editor, select contig
---> double-click on one letter will open this trace at this position and set cursor to exact this position !
double-click on the consensus line will open all traces at this position !
You can also see the "slack" by enable/disable "show cutoff";
Example ?
Try this very simple test data and verify this letter by letter:
% align_to_scf -f test.qry -o test.aln
--- test.qry ---
>F0FH8BE01EUM6Y <- name of read from sff archive
ATGCATCATG-ATGC <- fasta sequence of this read from ace file
ATGCATGCATGCATGC <- fasta sequence of this read from sff trace file
And you should get this output "test.aln" ( see also CAF format description ) :
>F0FH8BE01EUM6Y
Align_to_SCF 1 6 1 6
Align_to_SCF 7 10 8 11
Align_to_SCF 12 15 13 16
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