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  • #46
    Hi jstjohn,

    in the 'reads' folder there are 2 files generated per library.

    *.filtered.readpairs.singles.fasta extension is the filtered file during reading of the paired-read files. This file is filtered on paired-sequences containing N's. If one of the two sequences of a pair contains an 'N' character, the paired-read is discarded.

    *.foundpairedreads extension contains the paired-reads used for scaffolding. Keep in mind that we only use the edges of the contigs for mapping the reads, therefore less reads can be mapped (though we don't mind, because they are not very useful for scaffolding).

    Sorry that this was not clear.

    Boetsie

    Comment


    • #47
      I, too, would like to include BAC end sequences (Sanger seq) to scaffold pre-assembled contigs/scaffolds. I had trouble running Bambus (due to the requirement for a .contig file) and found SSPACE. However, Bowtie fails to map a majority of long reads due to indels/accumulation of mismatches in the long reads, so I would rather like to use (the best) mappings from bwa-swa, blat or another tool.

      Did anyone already solve the issue of either reading sam files, or convert those to the simple tab delimited format asked for by SSPACE? Would be great, as most aligners can output sam or be converted to that format with existing tools.

      Comment


      • #48
        Hi davfre,

        i'm sorry, i've not included this functionality yet. Also, It is not possible to include TAB-delimited files in SSPACE. Reason is that I did not have much time to work on this. I hope to do so in the near future, it is on my to-do list

        Kind regards,
        Boetsie

        Comment


        • #49
          Originally posted by e-summer-3 View Post
          SSPACE is very nice tool for us. Thank you for your good job.

          By the way, what should I call SSPACE?

          es es pace?
          es pace?
          es space?

          Regards.
          I'm sorry, i had not seen this question before, i must have missed it. You can call it 'es space'

          Boetsie

          Comment


          • #50
            input files

            Hi, I am just trying out SSPACE at the moment for a large genome (2.7Gb) using contigs assembled from abyss and a number of 3,5 and 10Kb mate pairs. Is there any way of getting SSPACE to accept compressed files as input?

            Comment


            • #51
              Originally posted by SLB View Post
              Hi, I am just trying out SSPACE at the moment for a large genome (2.7Gb) using contigs assembled from abyss and a number of 3,5 and 10Kb mate pairs. Is there any way of getting SSPACE to accept compressed files as input?
              hi SLB,

              i'm sorry but this is currently not possible.

              Boetsie

              Comment


              • #52
                I am just interested if anyone has been playing around with the parameters of SSPACE (k, a,) and has any insights.

                Cheers,

                Stephen

                Comment


                • #53
                  -t parameter

                  hi boetsie,

                  First, SSPACE is a great piece of software. Hands down, it's the easiest to use and most efficient scaffolder I've found and gives great results. Thanks for all your work.

                  I have a question about the -t parameter. After clipping up to -t bases, does SSPACE try to extended contigs again?

                  thanks,
                  ajtritt

                  Comment


                  • #54
                    Originally posted by ajtritt View Post
                    hi boetsie,

                    First, SSPACE is a great piece of software. Hands down, it's the easiest to use and most efficient scaffolder I've found and gives great results. Thanks for all your work.

                    I have a question about the -t parameter. After clipping up to -t bases, does SSPACE try to extended contigs again?

                    thanks,
                    ajtritt
                    Hi ajtritt,

                    thank you so much for this nice comment! Good that it gives great results for you, and I'm glad it could help.

                    To clearify about the trimming (-t option); SSPACE does not first clip up to -t bases. It first tries to extend. Then, if it can no longer extend a contig, it will try to trim bases and try to extend them again. This will go through until no more extension can be done as well as the trimming does not lead to further extension.

                    Kind regards,
                    Boetsie

                    Comment


                    • #55
                      Is it possible to change the bowtie options to allow mismatches?

                      Comment


                      • #56
                        Originally posted by SLB View Post
                        Is it possible to change the bowtie options to allow mismatches?
                        Hi SLB,

                        At the moment not, but in the next version i'm planning to include this option as well as multithreading bowtie.

                        For the moment, you can change the code and do it yourself . Go to the 'bin' directory and open the file MapWithBowtie.pl. Now go the lines starting with 'system'

                        Change the -v 0 to your required number of gaps, for example -v 2 allows two gaps.

                        For gapped mapping of the reads on the contigs for extension, change the first line starting with system("$bowtiepath ...
                        For gapped mapping of the reads on the contigs for scaffolding, change the second line starting with system("$bowtiepath ...

                        Boetsie

                        Comment


                        • #57
                          Hi Boetsie,

                          Thanks a million.

                          Cheers,

                          Stephen

                          Originally posted by boetsie View Post
                          Hi SLB,

                          At the moment not, but in the next version i'm planning to include this option as well as multithreading bowtie.

                          For the moment, you can change the code and do it yourself . Go to the 'bin' directory and open the file MapWithBowtie.pl. Now go the lines starting with 'system'

                          Change the -v 0 to your required number of gaps, for example -v 2 allows two gaps.

                          For gapped mapping of the reads on the contigs for extension, change the first line starting with system("$bowtiepath ...
                          For gapped mapping of the reads on the contigs for scaffolding, change the second line starting with system("$bowtiepath ...

                          Boetsie

                          Comment


                          • #58
                            Hi Boetie,

                            Do you plan to include the use of SAM/BAM as output instead of the default bowtie, that way you clould dropin all sam/bam capable aligners, like BWA (for longer reads with the sw option), Smalt http://www.sanger.ac.uk/resources/software/smalt/
                            or Stampy http://www.well.ox.ac.uk/project-stampy
                            and probably a full bag of other aligners.

                            Comment


                            • #59
                              Hi Vidja,

                              yes, i'm currently working on this though i don't have much time. Thank you for the suggestion of BWA for longer reads! I hope I can include more aligners.

                              Boetsie

                              Originally posted by VidJa View Post
                              Hi Boetie,

                              Do you plan to include the use of SAM/BAM as output instead of the default bowtie, that way you clould dropin all sam/bam capable aligners, like BWA (for longer reads with the sw option), Smalt http://www.sanger.ac.uk/resources/software/smalt/
                              or Stampy http://www.well.ox.ac.uk/project-stampy
                              and probably a full bag of other aligners.

                              Comment


                              • #60
                                edited after solution
                                Last edited by KanyeDidIt; 06-08-2011, 08:42 AM. Reason: solved

                                Comment

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