Originally posted by sundar
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need to view the extract conig file
Hi all, i can extract the best contig file by using a perl program .but i wanna view the extracted contig file.
Need help
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Originally posted by sundar View PostHi farhat,
I wanna know ,how to extract contig file ,I am running velvet algorithm , i got .afg format, that i have viewed in hawkeye .,and i wanna extract specific contig .can you help me on that, ??? it would be wonder if i get the positive reply from you
thanks
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Originally posted by Torst View PostCan you be a bit more precise on what you require?
A FASTA file is just a bunch of sequences with an ID and a description.
What form do you want the ACE file to take?
I am having the doubt in denovo assembly, shall i ask?
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Originally posted by Farhat View PostIs there a program to convert a Fasta file to an Ace assembly file? While googling I came across references to fasta2ace.pl but no program itself.
Thanks.
I wanna know ,how to extract contig file ,I am running velvet algorithm , i got .afg format, that i have viewed in hawkeye .,and i wanna extract specific contig .can you help me on that, ??? it would be wonder if i get the positive reply from you
thanks
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Originally posted by jkbonfield View PostThis still makes no sense.
ACE is an assembly output, while fasta is just a bunch of sequences with no assembly information. Are you asking for advice on what assembler to use? This will obviously depend a lot on the type of data and whether you want a denovo or mapped assembly.
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Originally posted by jkbonfield View PostGetting off-topic, sorry.
However MAF looks like a nice format. The problems of random ordering of data in CAF and the complete lack of sequence quality in ACE is one reason why I produced BAF, although it never really went anywhere and I only use it locally as an interchange format.
Originally posted by jkbonfield View PostCertainly it's true that ACE and CAF are very cumbersome for next-gen data, while SAM/BAM have other major issues when it comes to mixed technologies (such as not supporting older capillary style assemblies with potentially more than two sequences per template).
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Getting off-topic, sorry.
However MAF looks like a nice format. The problems of random ordering of data in CAF and the complete lack of sequence quality in ACE is one reason why I produced BAF, although it never really went anywhere and I only use it locally as an interchange format.
Certainly it's true that ACE and CAF are very cumbersome for next-gen data, while SAM/BAM have other major issues when it comes to mixed technologies (such as not supporting older capillary style assemblies with potentially more than two sequences per template).
A good find. :-)
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Originally posted by jkbonfield View PostPS. Contrary to above, I don't believe ACE supports quality values. At least I've never seen any - instead the authors of ace preferred to store qualities in "phd" files (in possibly the most inefficient format known to man). I'd love to be wrong on this though as it'll make my life easier. :-)
P.S. The MIRA assembly format (MAF, which is a bit like ACE), stores both - using FASTQ like encoding which is much more space efficient:
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This still makes no sense.
ACE is an assembly output, while fasta is just a bunch of sequences with no assembly information. Are you asking for advice on what assembler to use? This will obviously depend a lot on the type of data and whether you want a denovo or mapped assembly.
James
PS. Contrary to above, I don't believe ACE supports quality values. At least I've never seen any - instead the authors of ace preferred to store qualities in "phd" files (in possibly the most inefficient format known to man). I'd love to be wrong on this though as it'll make my life easier. :-)
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I'm looking for exactly the same thing for eagleview too!!
Would you mind sharing your script with me? I'll send you a message shortly. Thanks!
Jia
Originally posted by Farhat View PostYes, but it is not very mature though and has limitations. It works fine with Eagleview but there seem to be issues making it work with pbShort. If you want it, PM me with your email.
-F
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Originally posted by bioinfosm View PostThats great !
I started writing a script of my own, but then got on to other things
Farhat - is it possible for you to share the script for format conversion?
-F
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Originally posted by Farhat View PostThanks for the replies. Yes, I realize the Fasta File by itself doesn't have enough information to construct the ACE file. I wrote my own script to take in a FASTA file, a FASTQ quality file and the output from a SOAP or ELAND aligner and convert that to ACE which does work with EagleView.
I started writing a script of my own, but then got on to other things
Farhat - is it possible for you to share the script for format conversion?
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Thanks for the replies. Yes, I realize the Fasta File by itself doesn't have enough information to construct the ACE file. I wrote my own script to take in a FASTA file, a FASTQ quality file and the output from a SOAP or ELAND aligner and convert that to ACE which does work with EagleView.
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