User: d-cameron
d-cameron • 2.1k
- Reputation:
- 2,120
- Status:
- Trusted
- Location:
- Australia
- Last seen:
- 3 days, 22 hours ago
- Joined:
- 4 years, 4 months ago
- Email:
- d***************@gmail.com
Posts by d-cameron
<prev
• 237 results •
page 1 of 24 •
next >
0
votes
1
answer
169
views
1
answers
... If a previous analysis was done, why aren't you using the bam files from that analysis? ...
written 18 days ago by
d-cameron • 2.1k
2
votes
1
answer
169
views
1
answers
... Sequence alignment is an [embarrassingly parallel][1] computational task. That is, performance of bwa scales (almost) linearly with the number of threads provided. If you have a 24 core machine, you gain no benefit from running 3 8-thread bwa tasks in parallel instead of just running a single 24 th ...
written 18 days ago by
d-cameron • 2.1k
2
votes
1
answer
200
views
1
answers
... 1,500 patients is an aweful lot of patients to have the same "rare" disease. Are these 1500 different rare diseases or all the one disease?
The analysis I've seen done on rare diseases have used family trees of affected/not affected to prune the massive noise that you'll get by comparing population ...
written 4 months ago by
d-cameron • 2.1k
0
votes
1
answer
185
views
1
answers
... There are many, many SAM files where the content does not conform to the SAM specifications.
In the case of TLEN, the TLEN definition was changed in a specification update but many tools (including GATK) were not updated to reflect this. The spec themselves have recently changed to acknowledge that ...
written 5 months ago by
d-cameron • 2.1k
0
votes
1
answer
273
views
1
answers
... Part of the problem is that many of the germline events are in regions that are difficult to call (microsattelite expansions are a good example of this). Have you considered using tools other than Delly?
There have been a pair of benchmarking papers that came out recently
https://genomebiology.bio ...
written 5 months ago by
d-cameron • 2.1k
0
votes
1
answer
273
views
1
answers
... If you don't care where they are inserted then you're actually asking a different question. What you want to be asking is how many copy number variants (do you only care about gain or loss as well?) there exist in a human genome. This information is readily available in database such as dgv (http:// ...
written 5 months ago by
d-cameron • 2.1k
0
votes
1
answer
273
views
1
answers
... At a high level, there are two classes of rearrangement detection. Those relying on copy number, and those relying on breakpoint detection.
>Usually people refer to all interspersed duplications as "segmental duplcations"
These are typically called by copy number callers. Such segmental duplica ...
written 5 months ago by
d-cameron • 2.1k
0
votes
1
answer
426
views
1
answers
... > Unfortunately we can't really identify the correct structure after the insertion.
That does seem unusual. If you don't have any other compensating breakpoints, those calls indicate that the transgene is inserted on a double minute containing it and 7:28985942-36210528. The next steps I'd take ...
written 6 months ago by
d-cameron • 2.1k
1
vote
1
answer
622
views
1
answers
... The primary alignnent is not always the "left-most" on the query. This behaviour can be changed by supplying the "-5" flag in which case the alignment with the smallest coordinate will be reported as the primary. ...
written 8 months ago by
d-cameron • 2.1k
0
votes
1
answer
622
views
1
answers
... swbarnes2 answered your question regarding secondary alignments, but not supplementary alignments.
> For chimeric reads (i.e for this example true split-reads that for SV informative) the difference between secondary and supplementary is semantic, a secondary alignment would map to another posit ...
written 8 months ago by
d-cameron • 2.1k
Latest awards to d-cameron
Scholar
18 days ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Scholar
4 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Popular Question
8 months ago,
created a question with more than 1,000 views.
For What are the sematics of containing bwa split read alignments?
Commentator
8 months ago,
created a comment with at least 3 up-votes.
For C: Deciding on a Variant Caller
Scholar
9 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Scholar
12 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Popular Question
12 months ago,
created a question with more than 1,000 views.
For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Modernising the FASTQ Format
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Modernising the FASTQ Format
Supporter
14 months ago,
voted at least 25 times.
Popular Question
14 months ago,
created a question with more than 1,000 views.
For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Teacher
19 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Scholar
20 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Scholar
21 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Scholar
21 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Scholar
22 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Scholar
22 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Teacher
22 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Scholar
22 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Teacher
22 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1191 users visited in the last hour