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 |
Quick followup:
Is this DNA-Seq data or bisulfite sequencing data?
I looked over the data information, and it does appear to be bisulfite sequencing data. I found this paragraph detailing the data:
"Massively parallel deep bisulfite sequencing of plasma cfDNA methylation in HCC
Published on 09 Jan 2017 - 00:14 by Reetta Holmila
In this study, we applied targeted massively parallel semiconductor sequencing to assess methylation on a panel of genes (FBLN1, HINT2, LAMC1, LTBP1, LTBP2, PSMA2, PSMA7, PXDN, TGFB1, UBE2L3, VIM and YWHAZ) in plasma circulating cell-free DNA (cfDNA) and to evaluate the potential of these genes as HCC biomarkers in two different series, one from France (42 HCC cases and 42 controls) and one from Thailand (42 HCC cases, 26 chronic liver disease cases and 42 controls). We also analyzed a set of HCC and adjacent tissues and liver cell lines to further compare with ‘The Cancer Genome Atlas’ (TCGA) data."
Link to that page: https://figshare.com/projects/Massively_parallel_deep_bisulfite_sequencing_of_plasma_cfDNA_methylation_in_HCC/18185
Also need to locate BAM files from sequencing of non-bisulfite converted samples from individuals with structural variations.
| Assignee | Anh Moss [ aduong ] | Ann Loraine [ aloraine ] |
Un-assigning as Ahn is moving on to her next rotation. Good luck with everything!
| Assignee | Ann Loraine [ aloraine ] |
| Status | In Progress [ 3 ] | Open [ 1 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Attachment | SoftClipRegion.png [ 14162 ] |
Data sets from genome sequencing saved in IGB Dropbox under "Jira issues" folder for this issue.
Data are from twitter thread w/ Brent Pedersen from Aaron Quinlan lab University of Utah. See attached.
Marking this as closed (for now) as we now have a good handle on how to get more data & where to find potential reviewers/representative users:
- Brent Pedersen, Quinlan lab (working on structural variants)
- Greenwood Genetics (human genetics clinic in South Carolina)
- Canadian Bioinformatics workshop on genomic medicine instructors & attendees (attended by Nowlan & Ann, 2018)
- Wake Forest human genetics and genomics faculty
- Steve Chervitz Trutane (Personalis)
- Clinical variant analysts (https://www.linkedin.com/in/shelly-sorrells-phd-2a46333b/)
| 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 ] |
Here is a link to the following dataset:
https://figshare.com/articles/BAM_and_BAI_files/4530707/1
Data posted by: Reetta Holmila: Massively parallel deep sequencing of plasma cfDNA methylation in HCC and controls (categories: biomarkers)
This page lists both the BAM and BAI files.