User: d-cameron

gravatar for d-cameron
d-cameron2.1k
Reputation:
2,150
Status:
Trusted
Location:
Australia
Last seen:
3 hours ago
Joined:
4 years, 7 months ago
Email:
d***************@gmail.com

Posts by d-cameron

<prev • 252 results • page 2 of 26 • next >
0
votes
1
answer
97
views
1
answers
Comment: C: Extract SV indicating pair-end reads
... I wouldn't be using 10 year old bioinformatics software unless it's been constantly updated over that period. BreakDancer is a perfect example of such a highly cited unmaintained SV caller. It performs terribly on read length is over 50bp and pretty much every tool is benchmarked against it and, uns ...
written 7 weeks ago by d-cameron2.1k
0
votes
1
answer
97
views
1
answers
Comment: C: Extract SV indicating pair-end reads
... > elif not read.is_proper_pair: FYI: you can't trust that flag to be set correctly by the aligner. Some aligners set it to true if the chromosome and orientation is correct, regardless of the distance between the read pairs. ...
written 7 weeks ago by d-cameron2.1k
1
vote
1
answer
97
views
1
answers
Answer: A: Extract SV indicating pair-end reads
... > Is there any existing tools that can do this kind of thing for me? There are many such tools. When I did a lit review for my thesis on SV calling 5 years ago, there were around ~40 general purpose SV callers. There's at least 70 now. I recommend chosing one of the callers that perform well (in ...
written 7 weeks ago by d-cameron2.1k
0
votes
2
answers
113
views
2
answers
Comment: C: fusion detection for DNA Sequencing data
... Inless you've got a weird aligner, or using non-default settings, unmapped reads will still be in the BAM file - they'll just be marked as unmapped. ...
written 7 weeks ago by d-cameron2.1k
0
votes
2
answers
113
views
2
answers
Answer: A: fusion detection for DNA Sequencing data
... I've had success with using GRIDSS on WGS as well as cancer panels with tiled introns. Haven't tried it on ctDNA. AFAIK, GRIDSS2/PURPLE/LINX (https://www.biorxiv.org/content/10.1101/781013v1) is the only toolset that will do compound (multi-breakpoint) fusion prediction from DNA-seq data, but it's ...
written 7 weeks ago by d-cameron2.1k
0
votes
1
answer
366
views
1
answers
Comment: C: bwa mem memory allocation, threads and nodes
... If a previous analysis was done, why aren't you using the bam files from that analysis? ...
written 3 months ago by d-cameron2.1k
2
votes
1
answer
366
views
1
answers
Answer: A: bwa mem memory allocation, threads and nodes
... 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 3 months ago by d-cameron2.1k
2
votes
1
answer
305
views
1
answers
Answer: A: Approach to structural variation analysis - case vs control
... 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 7 months ago by d-cameron2.1k
0
votes
1
answer
225
views
1
answers
Answer: A: value of TLEN not conforming to the SAM specifications
... 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 8 months ago by d-cameron2.1k
0
votes
1
answer
339
views
1
answers
Comment: C: Number of Tandem and Interspersed duplications
... 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 8 months ago by d-cameron2.1k

Latest awards to d-cameron

Scholar 20 days ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 3 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 7 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Popular Question 11 months ago, created a question with more than 1,000 views. For What are the sematics of containing bwa split read alignments?
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Deciding on a Variant Caller
Scholar 12 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Popular Question 15 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Scholar 15 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Modernising the FASTQ Format
Supporter 17 months ago, voted at least 25 times.
Popular Question 17 months ago, created a question with more than 1,000 views. For GRIDSS: the Genomic Rearrangement IDentification Software Suite
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 23 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 2.0 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 2.1 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 2.1 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Scholar 2.1 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 2.1 years ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1006 users visited in the last hour