User: Shaun Jackman
Shaun Jackman • 420
- Reputation:
- 420
- Status:
- Trusted
- Location:
- Vancouver, Canada
- Website:
- http://sjackman.ca/
- Twitter:
- @sjackman
- Scholar ID:
- Google Scholar Page
- Last seen:
- 4 days, 12 hours ago
- Joined:
- 6 years, 4 months ago
- Email:
- s*******@gmail.com
I live in Vancouver, Canada, where I’m a PhD student studying bioinformatics at the University of British Columbia with my supervisor, Inanc Birol. I work with the genome sequencing data of a variety of species, including human and the white spruce tree. I develop software that takes fragmented genome sequencing data and attempts to reassemble the original genome from which the short fragments were derived. My undergraduate degree is in computer engineering. I’m a programmer, an avid traveller, a singer, and an experimental amateur chef.
Posts by Shaun Jackman
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... NCBI now accepts annotations submitted in GFF3 format.
See https://www.ncbi.nlm.nih.gov/genbank/genomes_gff/ ...
written 22 days ago by
Shaun Jackman • 420
1
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1
answer
354
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1
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... The formula for ABySS is not in the brewsci/bio tap, but in the core tap.
brew install abyss
...
written 29 days ago by
Shaun Jackman • 420
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2
answers
2.5k
views
2
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... Also @ is ASCII 64 which is 64 - 33 = PHRED Q 31. The quality line can contain and begin with both + and @. ...
written 4 months ago by
Shaun Jackman • 420
4
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1
answer
1.1k
views
1
answers
... The default values for `mp` is `pe`, and the default value for `pe` is `lib`.
You want to use
`mp='D1MNAACXX_2 D1MNAACXX_3 D1MNAACXX_6 D1MNAACXX_7 D1MNAACXX_8 C1MLEACXX_3 C1MLEACXX_4'`.
Do you have have five different paired-end libraries, or five lanes of one library? If it's the latter, you oug ...
written 9 months ago by
Shaun Jackman • 420
0
votes
1
answer
1.1k
views
1
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Comment:
C: Assembly with mate-pairs issue
... > Is it possible that ABySS when mate-pair data is provided does not do any scaffolding with the paired-ends all together (and thus only uses the mate-pair info)?
Yes, that is possible. Please report the exact command line that you used for both assemblies. ...
written 9 months ago by
Shaun Jackman • 420
0
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2
answers
8.8k
views
2
answers
... Use `$'\t'`
```
grep '^#' in.vcf > out.vcf && grep -v '^#' in.vcf | LC_ALL=C sort -t $'\t' -k1,1 -k2,2n >> out.vcf
``` ...
written 18 months ago by
Shaun Jackman • 420
1
vote
2
answers
2.8k
views
2
answers
Comment:
C: ABySS assembly runs forever
... You can also specify the number of MPI processes and number of OpenMP threads separately using the abyss-pe parameters np and j respectively. For example
abyss-pe np=64 j=12
Use 64 MPI processes and 12 OpenMP threads.
...
written 3.2 years ago by
Shaun Jackman • 420
4
votes
2
answers
877
views
2
answers
... PathConsensus outputs the IUPAC ambiguity codes. Set either `a=1` or `p=1` to disable PathConsensus ambiguity codes. Note that this will also disable PopBubbles. You may prefer to simply replace ambiguity codes with an ACGT nucleotide or N after assembly, as Ben suggested.
See https://github.com/bc ...
written 3.3 years ago by
Shaun Jackman • 420
2
votes
1
answer
1.0k
views
1
answers
Answer:
A: Boost compile error
... Hi, solarese. Try instead
./configure --prefix=/myhome/mybin/abyss-1.9.0/bin CPPFLAGS=-I/myhome1/mybin/sparsehash-2.0.2/include --with-boost=/opt/apps/intel15/boost/1.55.0/x86_64/include CC=icc CXX=icpc
See https://github.com/bcgsc/abyss#compiling-abyss-from-source
Note that `-L` should not be p ...
written 3.3 years ago by
Shaun Jackman • 420
2
votes
1
answer
1.7k
views
1
answers
Answer:
A: Abyss genome assembly input
... > From reading the abyss logs, I noticed in the past there was parallel reading of multiple input fastq.gz files. Is it possible that since I just have two huge files now, I am not taking advantage of this parallel reading? And a significant amount of time is being used just to read in files?
Y ...
written 3.3 years ago by
Shaun Jackman • 420
Latest awards to Shaun Jackman
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: Running Abyss On Cluster With Time Limitations
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: Github Workflow For Bioinformatics Analysis
Supporter
2.4 years ago,
voted at least 25 times.
Student
3.2 years ago,
asked a question with at least 3 up-votes.
For Counting Read Support At A Particular Position Of A Bam File
Teacher
3.3 years ago,
created an answer with at least 3 up-votes.
For A: Running Abyss On Cluster With Time Limitations
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For Counting Read Support At A Particular Position Of A Bam File
Scholar
3.3 years ago,
created an answer that has been accepted.
For A: Scaffolding with Mate-Pairs Error
Scholar
3.3 years ago,
created an answer that has been accepted.
For A: Scaffolding with Mate-Pairs Error
Scholar
3.4 years ago,
created an answer that has been accepted.
For A: Scaffolding with Mate-Pairs Error
Autobiographer
4.6 years ago,
has more than 80 characters in the information field of the user's profile.
Teacher
5.2 years ago,
created an answer with at least 3 up-votes.
For A: Github Workflow For Bioinformatics Analysis
Teacher
6.1 years ago,
created an answer with at least 3 up-votes.
For A: Running Abyss On Cluster With Time Limitations
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