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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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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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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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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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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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
On the other hand, you just need the SCF file as you have already created the phd file ..
Sven
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Originally posted by rucyfa View Postthanks 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 ?
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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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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Originally posted by rucyfa View PostIs 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.
Sven
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