Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:1
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Epic Link:
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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.
Attachments
Activity
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
obtained files, extracted to fastq, aligning with tophat
alignments for some failed, possibly due to unexpected temporary cluster shutdown
re-running; see script "cleanUp.sh" for how it was done
alignments completed
next step is to process alignments and deploy to a QL site
this will be done under a separate Jira ticket
closing this
Search SRA with https://ewels.github.io/sra-explorer/