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Old 05-10-2010, 09:52 AM   #1
rucyfa
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Default For consed, how can i change a fasta file to a fake read?

I have some fasta file which i download from GENBANK, i want to change it to fake read in order to input to consed v19.0, very appreciate for giving me some information.
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Old 05-11-2010, 03:39 AM   #2
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As a read, fasta2Phd.perl (1), as a reference to align reads against, fasta2Ace.perl (2).
Both from Consed Package.

Mentioned in the docs...
(1)= 13.4) ADDING READS WITHOUT CHROMATOGRAM FILES
(2)= 9.66) Convert the fasta file to an assembly by typing

Sven
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Old 05-11-2010, 06:54 AM   #3
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I used "fasta2Phd.perl" to make some file , for exemple "consensus1.phd.1" and put them into "Phd_dir" , how can i use them? it said launch phredphrep.......
but in witch path? ../chromat_dir or ../phd_dir?
will i lose the old assemblage?
i just want to add a fasta sequence as a read.
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Old 05-11-2010, 09:21 AM   #4
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What have you done? What do you want achieve? Your description is poor.

$ echo consensus1 > fofn.fof

then "add new reads" in consed witj fofn.fof.

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Old 05-11-2010, 11:48 AM   #5
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ok, i have some fasta files , i want use them like .ab1 to close my contigs.(for example: consensus1.fasta)

then i generated a "consensus1.phd.1", next I do not know how to use them the same as I "add new reads" for .ab1 files to consed.

by you mean i should use command "$ echo consensus1.fasta > consensus1.fof" but not "ls consensus1.fasta > consensus1.fof", then "add new reads".

is this right?
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Old 05-11-2010, 12:09 PM   #6
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Everything before the extension ".phd.1" is relevant. In your case "consensus1".
It doesn't matter how you create your input lists; I used 'echo' in this example just because you only mentioned one sequence.

Have you tried it?

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Old 05-11-2010, 12:58 PM   #7
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my problem is i don't know where i should put this files.
in my mind: "consensus1.fasta" should be in "chromat_dir" , "consensus.phd.1" should be in "Phd_dir".
then start consed--> "add new reads"--> find "consensus1.fof" to add them.
is this right ?
i am not in lab, i will try it tomorrow.
sorry for disturbing you, i am good at windows but i never use linux before, so there is realy so much things i should to learn, thanks for you patience again.
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Old 05-11-2010, 08:32 PM   #8
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The important thing is 'phd_dir'. You don't need the fasta for assembly. If you need a trace file (aka chromatogram) for "editing purposes", use "mktrace" with your fasta file and put the result to 'chromat_dir'.

cheers,
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Old 05-17-2010, 07:59 AM   #9
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for using "mktrace", for example consenesus1.faste, i used a command line: mktrace consenesus1.faste consenesus1.scf
is this right ?
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Old 05-17-2010, 08:33 AM   #10
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in the documentation it said after "mktrace", i would have the perfect peaks, but why in my case there is only quality=15 ?
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Old 05-17-2010, 09:43 AM   #11
sklages
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well, perfect in terms of peak shaping.

If you don't like the default value 15, you need to change it in the sources, in mktrace.h:

Code:
#define BASE_QUALITY 15
Set it to another value and recompile ...

On the other hand, you just need the SCF file as you have already created the phd file ..

Sven
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Old 05-17-2010, 12:18 PM   #12
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thanks a lot.
I can't use these SCF as a AB1 file for "add new reads", every time i need use the command "phredPhrap" to reassembly again in order to reload these SCF, but i may loss some ancient scaffords, do you have any idea of this ?
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Old 05-18-2010, 02:28 AM   #13
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Quote:
Originally Posted by rucyfa View Post
thanks a lot.
I can't use these SCF as a AB1 file for "add new reads", every time i need use the command "phredPhrap" to reassembly again in order to reload these SCF, but i may loss some ancient scaffords, do you have any idea of this ?
What is the problem? I think, I didn't get it.

Make a list of your chromats of interest (fofn) and "AddNewReads" from within consed.

You should really consider working through the consed tutorial. You need to understand some basic work principles of consed.

Sven
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Old 05-18-2010, 04:29 AM   #14
rucyfa
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Is there a rule for naming the SCF files?
Very strange,Yesterday, i used 502.fasta to generate a 502.SCF, i can't use "add newreads" ,if not consed will give me a error message.
Today,i change the fasta name as YM0AAA09Y019FM1.fasta, then i used mktrace to generate a YM0AAA09Y019FM1.SCF file,I successfully used the "add newreads" function.
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Old 05-18-2010, 09:27 AM   #15
sklages
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Quote:
Originally Posted by rucyfa View Post
Is there a rule for naming the SCF files?
Very strange,Yesterday, i used 502.fasta to generate a 502.SCF, i can't use "add newreads" ,if not consed will give me a error message.
What did it say?

Quote:
Today,i change the fasta name as YM0AAA09Y019FM1.fasta, then i used mktrace to generate a YM0AAA09Y019FM1.SCF file,I successfully used the "add newreads" function.
How does your corresponding phd-file look like? What its name?

Sven
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