Hi,
We are having problems adding a subset of reads from a single 454 plate to an existing Sanger assembly using cross_match/consed. There are instructions for this in the consed documentation under 9.88) ADDING ADDITIONAL 454 OR SOLEXA READS as follows:
"If you want to add just a few 454 reads (not all of them in the sff
file), and you know the names of the 454 reads you want to add, you
can use a different method:
In edit_dir, create a file (e.g., reads.fof) that contains the names
of all the 454 reads you want to add. Suppose these are contained
within the sff file my454.sff
Run:
sff2scfAndPhd my454.sff reads.fof
This will create both scf files in ../chromat_dir and phd files in
../phd_dir."
So here's the problem. The program sff2scfAndPhd does not seem to exist in the consed tarball, and we can't find any references to it in the phred/phrap documentation either. Has anyone successfullly used this program/method? If so, where did you get it?
Any advice will be appreciated!
We are having problems adding a subset of reads from a single 454 plate to an existing Sanger assembly using cross_match/consed. There are instructions for this in the consed documentation under 9.88) ADDING ADDITIONAL 454 OR SOLEXA READS as follows:
"If you want to add just a few 454 reads (not all of them in the sff
file), and you know the names of the 454 reads you want to add, you
can use a different method:
In edit_dir, create a file (e.g., reads.fof) that contains the names
of all the 454 reads you want to add. Suppose these are contained
within the sff file my454.sff
Run:
sff2scfAndPhd my454.sff reads.fof
This will create both scf files in ../chromat_dir and phd files in
../phd_dir."
So here's the problem. The program sff2scfAndPhd does not seem to exist in the consed tarball, and we can't find any references to it in the phred/phrap documentation either. Has anyone successfullly used this program/method? If so, where did you get it?
Any advice will be appreciated!
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