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  1. IGB
  2. IGBF-1625

Obtain and document fastq sequence data for breast cancer

        Details

        • Type: Bug
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Story Points:
          1
        • Epic Link:
        • Sprint:
          Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Spring 2019 Sprint 6

          Description

          Bioinformatics.ca (bioinformatics training nexus in Canada) offers an a workshop on bioinformatics of cancer that focuses on sequencing applications.

          In Module 4 (see: https://bioinformaticsdotca.github.io/BiCG_2018_mod3_mapping) students download data from a breast cancer tumor sample (HCC1395) and align it to a 1000 genomes reference using bwa.

          However, because of time and space limitations, students only align a portion of the data.

          In this task, identify the "raw" sequence data and download the full data set onto the UNC Charlotte cluster. Also, look into whether it is OK for us to align the data and then distribute it as an freely available data set for IGB user outreach and training.

          Make a note in the Comments indicating:

          • Where you obtained the data (add links)
          • Where you put it on the cluster (indicate file path)

          Any additional notes should be added to a google doc. Ask Dr. Loraine to create a starter doc for this.

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              ann.loraine Ann Loraine created issue -
              ann.loraine Ann Loraine made changes -
              Field Original Value New Value
              Epic Link IGBF-1478 [ 17563 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Sprint Spring 2019 Sprint 3 [ 61 ] Spring 2019 Sprint 3, Spring 2019 Sprint 4 [ 61, 62 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Status Open [ 1 ] In Progress [ 3 ]
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]
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              ann.loraine Ann Loraine added a comment -

              Search SRA with https://ewels.github.io/sra-explorer/

              Show
              ann.loraine Ann Loraine added a comment - Search SRA with https://ewels.github.io/sra-explorer/
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              ann.loraine Ann Loraine added a comment -

              Link: https://www.ncbi.nlm.nih.gov/sra/SRR2532336
              Data are 50 bp PE. Too short. Don't use.
              Using this instead: https://bitbucket.org/lorainelab/breast-cancer-srp157974

              Show
              ann.loraine Ann Loraine added a comment - Link: https://www.ncbi.nlm.nih.gov/sra/SRR2532336 Data are 50 bp PE. Too short. Don't use. Using this instead: https://bitbucket.org/lorainelab/breast-cancer-srp157974
              ann.loraine Ann Loraine made changes -
              Summary Obtain and document fastq sequence data for breast cancer cell line Obtain and document fastq sequence data for breast cancer
              ann.loraine Ann Loraine made changes -
              Status In Progress [ 3 ] Open [ 1 ]
              ann.loraine Ann Loraine made changes -
              Sprint Spring 2019 Sprint 3, Spring 2019 Sprint 4 [ 61, 62 ] Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 61, 62, 63 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
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              ann.loraine Ann Loraine added a comment -

              obtained files, extracted to fastq, aligning with tophat

              Show
              ann.loraine Ann Loraine added a comment - obtained files, extracted to fastq, aligning with tophat
              ann.loraine Ann Loraine made changes -
              Status Open [ 1 ] In Progress [ 3 ]
              ann.loraine Ann Loraine made changes -
              Sprint Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 61, 62, 63 ] Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Spring 2019 Sprint 6 [ 61, 62, 63, 64 ]
              ann.loraine Ann Loraine made changes -
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              ann.loraine Ann Loraine added a comment -

              alignments for some failed, possibly due to unexpected temporary cluster shutdown
              re-running; see script "cleanUp.sh" for how it was done

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              ann.loraine Ann Loraine added a comment - alignments for some failed, possibly due to unexpected temporary cluster shutdown re-running; see script "cleanUp.sh" for how it was done
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              ann.loraine Ann Loraine added a comment -

              alignments completed

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              ann.loraine Ann Loraine added a comment - alignments completed
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              ann.loraine Ann Loraine added a comment -

              next step is to process alignments and deploy to a QL site
              this will be done under a separate Jira ticket
              closing this

              Show
              ann.loraine Ann Loraine added a comment - next step is to process alignments and deploy to a QL site this will be done under a separate Jira ticket closing this
              ann.loraine Ann Loraine made changes -
              Resolution Done [ 10000 ]
              Status In Progress [ 3 ] Closed [ 6 ]
              ann.loraine Ann Loraine made changes -
              Workflow Loraine Lab Workflow [ 18346 ] Fall 2019 Workflow Update [ 20076 ]
              ann.loraine Ann Loraine made changes -
              Workflow Fall 2019 Workflow Update [ 20076 ] Revised Fall 2019 Workflow Update [ 22210 ]

                People

                • Assignee:
                  ann.loraine Ann Loraine
                  Reporter:
                  ann.loraine Ann Loraine
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                  Dates

                  • Created:
                    Updated:
                    Resolved: