UGENE
  1. UGENE
  2. UGENE-3324

Sanger reads quality control and alignment

    Details

    • Epic Name:
      Sanger
    • Sprint:
      DEV-29/01/2015, DEV-12/02/2015
    • Affect Type:
      Userdefined

      Description

      Think on how to improve the following procedure:

      1. A region is sequenced with Sanger. There are several ABI files for it. The reads are shifted and some of them are reversed.
      2. The quality of ends of the regions is poor, so the ends of the reads must be trimmed.
      3. Then the reads must be aligned. The direction of the reads must be taken into account.

      See also: http://ugene.unipro.ru/forum/YaBB.pl?num=1406104444

        Issue Links

          Issues in Epic

            Activity

            Hide
            Olga Golosova
            added a comment -

            One more request about aligning/editing chromotograms:
            "I have recently downloaded your software for the purpose of editing and assembling sequences around 600-1000bp long. The software I am used to or this is sequencher and I was wondering if your software had the tools to enable me to edit both forward and reverse sequences (which have been assembled) by observing the chromatograms of each sequence?"

            Show
            Olga Golosova
            added a comment - One more request about aligning/editing chromotograms: "I have recently downloaded your software for the purpose of editing and assembling sequences around 600-1000bp long. The software I am used to or this is sequencher and I was wondering if your software had the tools to enable me to edit both forward and reverse sequences (which have been assembled) by observing the chromatograms of each sequence?"
            Hide
            Olga Golosova
            added a comment -

            One more request. Vector NTI is currently used by the user.
            "It is handy to see the alignment and forward/reverse chromatograms at the same time..."

            Show
            Olga Golosova
            added a comment - One more request. Vector NTI is currently used by the user. "It is handy to see the alignment and forward/reverse chromatograms at the same time..."
            Hide
            Olga Golosova
            added a comment -

            A reference to one more request (the old one): http://ugene.unipro.ru/forum/YaBB.pl?num=1416477334/0

            Show
            Olga Golosova
            added a comment - A reference to one more request (the old one): http://ugene.unipro.ru/forum/YaBB.pl?num=1416477334/0
            Hide
            Olga Golosova
            added a comment -

            A comment from UGENE-1352 which is a duplicate of this issue:
            "See Sequencher(http://genecodes.com/) or SnapGene for more detail.
            The request is described in this discussion: http://vk.com/uniprougene?w=wall-74359225_134"

            Show
            Olga Golosova
            added a comment - A comment from UGENE-1352 which is a duplicate of this issue: "See Sequencher( http://genecodes.com/ ) or SnapGene for more detail. The request is described in this discussion: http://vk.com/uniprougene?w=wall-74359225_134 "
            Show
            Olga Golosova
            added a comment - See also: http://ugene.unipro.ru/forum/YaBB.pl?num=1406104444/21#21
            Hide
            Olga Golosova
            added a comment -

            See comment by a user: https://www.facebook.com/groups/ugene/permalink/1563852140550694/.

            I want to to view the possible amino acid sequence in a nucleotide multiple seq alignment. For example in Mesquite you can view the nucleotide alignment and at the top you can view the amino acid seq base on each codon.

            Show
            Olga Golosova
            added a comment - See comment by a user: https://www.facebook.com/groups/ugene/permalink/1563852140550694/ . I want to to view the possible amino acid sequence in a nucleotide multiple seq alignment. For example in Mesquite you can view the nucleotide alignment and at the top you can view the amino acid seq base on each codon.

              People

              • Assignee:
                Unassigned
                Reporter:
                Olga Golosova
              • Votes:
                1 Vote for this issue
                Watchers:
                2 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved:

                  Agile