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  1. IGB
  2. IGBF-3741

Align Trinity Contigs to SL4 & SL5 via BLAT

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Minor
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Goal is to visualize how the BLAT alignments look.
          To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

          But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

          The current blat command being used is this:

          blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
          /dev/null /dev/null -tileSize=11 -makeOoc=$

          {file}

          .11.ooc -repMatch=1024

          Script will point to proper reference genome files.
          And we will incorporate other parameters as Ann suggests.
          which are..........

            Attachments

              Activity

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              robofjoy Robert Reid created issue -
              robofjoy Robert Reid made changes -
              Field Original Value New Value
              Epic Link IGBF-2993 [ 21429 ]
              robofjoy Robert Reid made changes -
              Description
              Goal is to visualize how the BLAT alignments look.
              To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

              But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

              The current blat command being used is thisL

              {quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
                /dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc \
                -repMatch=1024{quote}

              Script will point to proper reference genome files.
              And we will incorporate other parameters as Ann suggests.
              which are..........               		Goal is to visualize how the BLAT alignments look.
              To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

              But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

              The current blat command being used is thisL

              {quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
                /dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc \
                -repMatch=1024{quote}

              Script will point to proper reference genome files.
              And we will incorporate other parameters as Ann suggests.
              which are..........
              Sprint Spring 10 [ 194 ]
              robofjoy Robert Reid made changes -
              Summary Align Trinity Contigs to SL$ & SL5 via BLAT Align Trinity Contigs to SL4 & SL5 via BLAT
              robofjoy Robert Reid made changes -
              Description Goal is to visualize how the BLAT alignments look.
              To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

              But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

              The current blat command being used is thisL

              {quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
                /dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc \
                -repMatch=1024{quote}

              Script will point to proper reference genome files.
              And we will incorporate other parameters as Ann suggests.
              which are..........               		Goal is to visualize how the BLAT alignments look.
              To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

              But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

              The current blat command being used is thisL

              {quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
                /dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc \
                repMatch=1024 {quote}

              Script will point to proper reference genome files.
              And we will incorporate other parameters as Ann suggests.
              which are..........
              robofjoy Robert Reid made changes -
              Description Goal is to visualize how the BLAT alignments look.
              To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

              But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

              The current blat command being used is thisL

              {quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
                /dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc \
                repMatch=1024 {quote}

              Script will point to proper reference genome files.
              And we will incorporate other parameters as Ann suggests.
              which are..........               		Goal is to visualize how the BLAT alignments look.
              To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

              But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

              The current blat command being used is thisL

              {quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
                /dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc -repMatch=1024 {quote}

              Script will point to proper reference genome files.
              And we will incorporate other parameters as Ann suggests.
              which are..........
              robofjoy Robert Reid made changes -
              Description Goal is to visualize how the BLAT alignments look.
              To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

              But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

              The current blat command being used is thisL

              {quote}blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
                /dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc -repMatch=1024 {quote}

              Script will point to proper reference genome files.
              And we will incorporate other parameters as Ann suggests.
              which are..........               		Goal is to visualize how the BLAT alignments look.
              To do this we need to align contigs to SL4 and SL5 genome (and not to CDS).

              But before we do this, we want to implement Ann's suggestions for blat parameters. (e.g., max intron size:10K)

              The current blat command being used is this:

              blat /projects/tomato_genome/db/SL5/SL5.cds.fa \
                /dev/null /dev/null -tileSize=11 -makeOoc=${file}.11.ooc -repMatch=1024

              Script will point to proper reference genome files.
              And we will incorporate other parameters as Ann suggests.
              which are..........
              ann.loraine Ann Loraine made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]
              ann.loraine Ann Loraine made changes -
              Sprint Spring 10 [ 194 ] Summer 1 [ 195 ]
              robofjoy Robert Reid made changes -
              Assignee Robert Reid [ robertreid ]
              robofjoy Robert Reid made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              robofjoy Robert Reid made changes -
              Assignee Robert Reid [ robertreid ] Brandon Benkick [ bbendick ]
              robofjoy Robert Reid made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              robofjoy Robert Reid made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              robofjoy Robert Reid made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              robofjoy Robert Reid made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              robofjoy Robert Reid made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              robofjoy Robert Reid made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
              robofjoy Robert Reid made changes -
              Resolution Done [ 10000 ]
              Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                People

                • Assignee:
                  bbendick Brandon Bendickson
                  Reporter:
                  robofjoy Robert Reid
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                  Dates

                  • Created:
                    Updated:
                    Resolved: