Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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?

  • #2
    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
    OHSU

    Comment


    • #3
      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.

      Comment


      • #4
        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, 02:01 AM. Reason: correct inaccuracy

        Comment


        • #5
          I want to convert ace file which contains thousands contigs to phd file at one time by consed, is there any good way?

          Comment


          • #6
            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

            Comment


            • #7
              @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

              Comment


              • #8
                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.

                Comment


                • #9
                  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

                  Comment


                  • #10
                    thanks^^^^^^^^^^^^^^

                    Comment


                    • #11
                      What's Consed's memory usage when open ACE file contains 10 million solexa reads ?

                      Who knowns the memory usage about Consed?

                      Comment


                      • #12
                        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.

                        Comment


                        • #13
                          @baohua100,

                          opening an ACE file with 6.5Mio reads (2Mb genome) used 5.5GB physical memory.

                          Comment


                          • #14
                            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, 03:28 AM.

                            Comment


                            • #15
                              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

                              Comment

                              Latest Articles

                              Collapse

                              • seqadmin
                                Strategies for Sequencing Challenging Samples
                                by seqadmin


                                Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                                03-22-2024, 06:39 AM
                              • seqadmin
                                Techniques and Challenges in Conservation Genomics
                                by seqadmin



                                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                                Avian Conservation
                                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                                03-08-2024, 10:41 AM

                              ad_right_rmr

                              Collapse

                              News

                              Collapse

                              Topics Statistics Last Post
                              Started by seqadmin, 03-27-2024, 06:37 PM
                              0 responses
                              13 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 03-27-2024, 06:07 PM
                              0 responses
                              11 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 03-22-2024, 10:03 AM
                              0 responses
                              53 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 03-21-2024, 07:32 AM
                              0 responses
                              69 views
                              0 likes
                              Last Post seqadmin  
                              Working...
                              X