Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Minor
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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:0.5
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Sprint:Fall 2018 Sprint 3
Description
Find real soft clip data for testing purposes. The ideal dataset would have the following:
-paired-end data
-data with known structural variants
-preferably aligned in BAM format
One user who uses soft clipping in their research suggested the following links:
http://jimb.stanford.edu/giab-resources/
https://toolbox.google.com/datasetsearch
Attachments
Issue Links
- relates to
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- Closed
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Activity
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Summary | Real soft clip data | Find real soft clip data |
| Description |
Look for real world data for soft clipping.
-pair-end would be great -with known structural variants -aligned as a BAM file, preferably |
Find real soft clip data for testing purposes. The ideal dataset would have the following:
-paired-end data -data with known structural variants -preferably aligned in BAM format One user who uses soft clipping in their research suggested the following links: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/NHGRI_Illumina300X_novoalign_bams/ ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/ |
| Description |
Find real soft clip data for testing purposes. The ideal dataset would have the following:
-paired-end data -data with known structural variants -preferably aligned in BAM format One user who uses soft clipping in their research suggested the following links: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/NHGRI_Illumina300X_novoalign_bams/ ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/ |
Find real soft clip data for testing purposes. The ideal dataset would have the following:
-paired-end data -data with known structural variants -preferably aligned in BAM format One user who uses soft clipping in their research suggested the following links: http://jimb.stanford.edu/giab-resources/ https://toolbox.google.com/datasetsearch |
| Assignee | Anh Moss [ aduong ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | In Progress [ 3 ] | Open [ 1 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Attachment | SoftClipRegion.png [ 14162 ] |
| Resolution | Done [ 10000 ] | |
| Status | In Progress [ 3 ] | Closed [ 6 ] |
| Summary | Find real soft clip data | Find example data sets where soft clipping reveals polymorphisms |
| Assignee | Ann Loraine [ aloraine ] | Anh Moss [ aduong ] |
| Workflow | Loraine Lab Workflow [ 18128 ] | Fall 2019 Workflow Update [ 19954 ] |
| Workflow | Fall 2019 Workflow Update [ 19954 ] | Revised Fall 2019 Workflow Update [ 22075 ] |