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Old 03-11-2009, 05:44 PM   #1
greigite
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Location: Cambridge, MA

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Posts: 141
Default Problem with adding 454 reads with cross_match

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!
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Old 03-11-2009, 11:36 PM   #2
sklages
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Location: Berlin, DE

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Posts: 628
Default

You may want to have a look at "Files fixed after consed released":

http://bozeman.mbt.washington.edu/co.../current_beta/

cheers,
Sven
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Old 03-13-2009, 04:05 PM   #3
greigite
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Posts: 141
Exclamation sff2scfAndPhd memory leak

Thanks for that link. We got the program and ran it on our sff file, but it appears to have a memory leak which rapidly ate up all available memory, then crashed. Has anyone successfully used this program?
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Old 05-14-2009, 04:51 PM   #4
TJK-OHSU
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Location: Portland, Oregon

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Default

Which version of Consed are you using?
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Old 05-31-2011, 09:28 AM   #5
ysockhwa
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Location: Malaysia

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Default Hi

Hi. I just join this forum.

I hope to learn more from this forum.

I am learning Consed but I do have problem when I try on this command (sff2scfAndPhd). I am using Conced v19.
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Old 05-31-2011, 09:45 AM   #6
TJK-OHSU
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Default

From the Consed ReadMe for v.19
080821 of sff2scf (supplied with this version--discard previous
versions or you will be sorry. Type "sff2scf -v" and it should
say the correct version. If it instead says:
"Error: Unable to open SCF file: ../chromat_dir/-v", your
version is old and should be discarded.
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Old 06-02-2011, 12:29 PM   #7
ysockhwa
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Default Thanks

Thanks. I will check on it. Hopefully it works.
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