Details
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Type: Task
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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:None
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Story Points:0.25
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Epic Link:
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Sprint:Fall 5 2021 Oct 11 - Oct 22
Description
Some confusions have emerged regarding the strandedness of RNA-Seq data sets from tomato. Investigate tooling that can detect this in a dataset.
Attachments
Activity
Ann Loraine
created issue -
Ann Loraine
made changes -
Field | Original Value | New Value |
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Epic Link | IGBF-2323 [ 18477 ] |
Ann Loraine
made changes -
Sprint | Fall 5 2021 Oct 11 - Oct 22 [ 131 ] |
Ann Loraine
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Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Ann Loraine
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Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
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Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Ann Loraine
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Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Ann Loraine
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Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Ann Loraine
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Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Ann Loraine
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Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
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Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Ann Loraine
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Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Ann Loraine
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Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
RSeqQC is a suite of python programs for analyzing RNA-Seq data. One of these programs is "infer_experiment.py", which can detect whether a stranded library synthesis protocol was used.
To install and then use RSeqQC, use pip3 to install virtualenv for your user. Then start the virtual environment and install RSeqQC and its dependencies, using pip3.