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Old 05-05-2010, 05:23 AM   #1
rucyfa
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Question consed 19.0 adding new reads problem, realy need help

i have some Sanger sequencing chromatogrames result, i do not know how to insert these results into consed v19.0, it is for genome finishing, Someone can tell me every step? I would be very grateful.

and i want to know how to creat a *.fof file for those ab1 chromatogrames, thanks a lot.
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Old 05-05-2010, 12:05 PM   #2
sklages
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Hi rucyfa,

you should really walk through the documentation of consed as it will answer most of your (actual and upcoming) questions:
http://bozeman.mbt.washington.edu/co...EADME.19.0.txt

short: you need to basecall your ab1 files (usually done with phred or tractuner) and then assemble the sequences using phrap; this is usually done with the phredPhrap script provided with the package. You can then load the alignment (ACE) file into consed for further reviewing/finishing.

If you then run into problems ask your specific questions or post to the consed mailing list (phui).

btw, 'ls *.ab1 > myFiles.fof' will create a fof list ...

cheers,
Sven

Last edited by sklages; 05-05-2010 at 12:08 PM. Reason: forgot to mention the ace file :-)
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Old 05-05-2010, 12:45 PM   #3
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well, thanks a lot, and i read the readme, i think my question is within 9.138) ADD NEW READS (SANGER - NOT SOLEXA OR 454)
it said "copy the new chromatograms into the chromat_dir
directory: cp ../chromats_to_add/* ../chromat_dir"
I put all my ab1 files into the "chromat_dir" folder, and create a fof list which i put into "edit_dir folder", but it dose not work.
shoud i do basecall all my new ab1 files again with phred ?
Sorry to bother you again..........
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Old 05-05-2010, 12:49 PM   #4
sklages
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Quote:
Originally Posted by rucyfa View Post
well, thanks a lot, and i read the readme, i think my question is within 9.138) ADD NEW READS (SANGER - NOT SOLEXA OR 454)
it said "copy the new chromatograms into the chromat_dir
directory: cp ../chromats_to_add/* ../chromat_dir"
I put all my ab1 files into the "chromat_dir" folder, and create a fof list which i put into "edit_dir folder", but it dose not work.
shoud i do basecall all my new ab1 files again with phred ?
Sorry to bother you again..........
What did you do?
What "does not work"?
What errors do you get?
Do you already have an assembly and want to add some reads or do you want to assemble some reads from scratch?

Still too many questions .. ;-)

Sven
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Old 05-05-2010, 12:57 PM   #5
rucyfa
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sorry, I never used consed before.
yes, i have already an assembly, and i want to add some new reads, what can i do ?
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Old 05-05-2010, 01:09 PM   #6
sklages
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If you now have your list 'myFiles.fof' go ahead in the docs, subsitute 'reads_to_add.fof' with 'myFiles.fof',

Quote:
9.138) ADD NEW READS (SANGER--NOT SOLEXA OR 454)
[...]
On the Main Window, click on the Add New Reads button. There will
appear a list of files ending with .fof. These are files that contain
lists of chromatograms. Double click on 'reads_to_add.fof' (Accept
the defaults for the other options in this window.)

There should be lots of progress output in the xterm from which you
started Consed. When it completes, there will be a Reads Added Window
popup with a report of which reads were added.
Finally see if everythings goes fine .. if not:

Quote:
If you get an error message, look carefully at the full error message
in the xterm to diagnose the problem. Probably there is some mistake
in how you installed Consed. See INSTALLING CONSED (above).
Until here really nothing special ...

cheers,
Sven
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Old 05-05-2010, 01:24 PM   #7
rucyfa
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yee....
it should be nothing wrong, but it gives me a error message, i will show you tomorrow,
Thank you for your patience to answer and good night.
and again, to confirm fof file: in the new reads folder which contains my new ab1 files, i used command 'ls *.ab1 > myFiles.fof' to generate a fof file, then i put it into edit_dir folder, is all this right ?
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Old 05-06-2010, 05:40 AM   #8
rucyfa
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Something went wrong running /usr/local/genome/bin/addReads2Consed.perl GenoscopeRhelvetica.fasta.screen.ace.35 /Users/nfs/dongxin/GenoscopeRhelvetica/newreads001/myreads001.fof addReadsAlignments153028. Gave error code 512 which means Unknown error: 512

this is the message for me, i know somethings wrong, do you have un idea for this?
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Old 05-06-2010, 06:02 AM   #9
sklages
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I still don't know what you have done and how your fof really look like,

have you checked for cross_match and phred being installed (properly)?

Sven
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Old 05-08-2010, 09:45 AM   #10
rucyfa
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U R right, evreything goes fine. I made a mistake, i find a read whose name with a space in it, therefore, always error process, anyway thanks a lot, I started to master the software
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