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Old 03-13-2009, 06:28 PM   #1
anyone1985
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Default how convert ace to phd without consed?

I have an ace file generated by amos2ace, but it can not be opened by consed. what i want is a phd file coming from the ace file. So can any tools convert the ace file to phd file?
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Old 03-19-2009, 11:34 AM   #2
TJK-OHSU
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Default RE: how convert ace to phd without consed?

Consed comes with several utility programs:
ace2Fasta.perl generates a fasta file (actually I think it is fastq)
then
fasta2Phd.perl would give you the phd file you want.
You need to get these from the good people at U. Washington though.
Tom K
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Old 03-22-2009, 12:05 AM   #3
anyone1985
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I got consed v19, and mapped the Solexa reads to my reference sequence. It work well. But I had more two hundred contigs and how can i convert the ace file to phd files seperately by consed/phrap at one time? I saw that every contig could consert to phd file by file->export consesus sequence with options.
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Old 03-22-2009, 01:46 AM   #4
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Default Viewing Ace Files

There are several open source software to view the alignments in the assembled contigs: Eagleview (Marth Lab, Boston College). More are listed in other posts. If you want to edit and manipulate the contigs try the commercial software Lasergene SeqMan from DNAStar. Both programs have trouble with large numbers of reads. I don't know how Consed works with 5 Mio reads (or more) aligned to a reference sequence.

Last edited by cabauser; 03-22-2009 at 02:01 AM. Reason: correct inaccuracy
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Old 03-22-2009, 05:46 PM   #5
anyone1985
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I want to convert ace file which contains thousands contigs to phd file at one time by consed, is there any good way?
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Old 03-22-2009, 09:26 PM   #6
Rao
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I've no idea about consed... but we can use BioPerl for this...
see this link for more on this... http://www.bioperl.org/wiki/Module:Bio::SeqIO
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Old 03-23-2009, 11:06 AM   #7
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@anyone1985,

ace format is an alignment format, phd isn't. What do you want to achieve?

You have mapped your solexa reads against a reference sequence and get a few thousand contigs? Optimise your reference

If you just want to reassemble your contigs, convert ace to fasta and use phrap and/or cap3 directly?

Sven
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Old 03-23-2009, 05:40 PM   #8
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I just assemble my solexa data with velvet, and get about 240 contigs larger than 500. Then, I map the solexa data to the contigs using the consed/addSolexaReads.perl to get a contigs with quality. Now, I want to convert the ace file to phd file individually. The consed can export the phd file only one at a time, I just want to know how to convert it all at a time.
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Old 03-23-2009, 08:35 PM   #9
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Well, I think you need to write a script on your own, which parses the ACE files and dumps PHD. That's probably the fastest way. No other idea, sorry.

Sven
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Old 03-24-2009, 12:28 AM   #10
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thanks^^^^^^^^^^^^^^
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Old 03-24-2009, 08:35 PM   #11
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What's Consed's memory usage when open ACE file contains 10 million solexa reads ?

Who knowns the memory usage about Consed?
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Old 03-24-2009, 11:01 PM   #12
anyone1985
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To be honest, I maped my reference sequence with about 7 million reads, which is about half of my data. I divided the reference into six files, and the server that i use worked well. If i put them together, the program would be killed. My server is inspur with 8 G menory, about 4 G swap.
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Old 03-25-2009, 02:13 AM   #13
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@baohua100,

opening an ACE file with 6.5Mio reads (2Mb genome) used 5.5GB physical memory.
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Old 03-25-2009, 03:25 AM   #14
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Quote:
Originally Posted by sklages View Post
@baohua100,

opening an ACE file with 6.5Mio reads (2Mb genome) used 5.5GB physical memory.
what's the version of consed ? 19.0 ?

what's the length of your read?

what's the cpu time load this ACE file?

thanks!

Last edited by baohua100; 03-25-2009 at 03:28 AM.
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Old 03-25-2009, 04:25 AM   #15
sklages
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Quote:
Originally Posted by baohua100 View Post
what's the version of consed ? 19.0 ?

what's the length of your read?

what's the cpu time load this ACE file?

thanks!
v19.00, 32b PE, 6min to open, didn't check cpu time
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Old 03-25-2009, 12:55 PM   #16
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Quote:
Originally Posted by anyone1985 View Post
I just assemble my solexa data with velvet, and get about 240 contigs larger than 500. Then, I map the solexa data to the contigs using the consed/addSolexaReads.perl to get a contigs with quality. Now, I want to convert the ace file to phd file individually. The consed can export the phd file only one at a time, I just want to know how to convert it all at a time.
If you want to get the consensus contig sequences as phd files you could export all contigs from Consed into a multifasta, then use lib2Phd.perl to convert them into phd files. You'd have to write your own script to get the consensus contig qualities into the fake phd files as lib2Phd.perl just puts a score of 20 for all bases.
If you wanted to get your solexa reads into phd files you could also use lib2Phd.perl on the read fasta file, then write your own script to pop Solexa qualities into these fake phd files. I did this with 454 reads and it works well to visualize read qualities in Consed.
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Old 03-25-2009, 04:40 PM   #17
anyone1985
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Thanks. I am trying.......

Quote:
Originally Posted by greigite View Post
If you want to get the consensus contig sequences as phd files you could export all contigs from Consed into a multifasta, then use lib2Phd.perl to convert them into phd files. You'd have to write your own script to get the consensus contig qualities into the fake phd files as lib2Phd.perl just puts a score of 20 for all bases.
If you wanted to get your solexa reads into phd files you could also use lib2Phd.perl on the read fasta file, then write your own script to pop Solexa qualities into these fake phd files. I did this with 454 reads and it works well to visualize read qualities in Consed.
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