User: Shaun Jackman
Shaun Jackman • 340
- Reputation:
- 340
- Status:
- Trusted
- Location:
- Vancouver, Canada
- Website:
- http://sjackman.ca/
- Twitter:
- @sjackman
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 months, 1 week ago
- Joined:
- 5 years, 1 month 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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... Use `$'\t'`
```
grep '^#' in.vcf > out.vcf && grep -v '^#' in.vcf | LC_ALL=C sort -t $'\t' -k1,1 -k2,2n >> out.vcf
``` ...
written 3 months ago by
Shaun Jackman • 340
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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 24 months ago by
Shaun Jackman • 340
4
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2
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627
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... 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 2.0 years ago by
Shaun Jackman • 340
2
votes
1
answer
680
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1
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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 2.0 years ago by
Shaun Jackman • 340
2
votes
1
answer
902
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 2.1 years ago by
Shaun Jackman • 340
0
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2
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625
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2
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... I'm pretty sure that you've exceed the available memory. If you run ABySS with `abyss-pe v=-v` it will tell you how much memory each node is using. If it's already running, run `top` or `ps aux |grep ABYSS`. For a large genome, be sure to use the MPI version by specifying `abyss-pe np=12` where 12 i ...
written 2.1 years ago by
Shaun Jackman • 340
0
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0
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567
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0
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Comment:
C: Abyss 1.5.2: MergePaths failed
... Please post a gist of these two files:
snow-4.adj snow-4.path1
...
written 2.1 years ago by
Shaun Jackman • 340
0
votes
1
answer
970
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1
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Comment:
C: Scaffolding with Mate-Pairs Error
... Happy to help. Watch that white space! =)
...
written 2.1 years ago by
Shaun Jackman • 340
2
votes
1
answer
970
views
1
answers
... Hi, Graham. Thanks for your detailed report. It makes your question easy to answer. You're missing an important space between a single quote and a backslash. Change this line:
lib='pe300_1 pe300_2 pe400_2 pe500_1 pe500_2' mp='mp_1 mp_2'\
to
lib='pe300_1 pe300_2 pe400_2 pe500_1 pe500_2' mp='mp_1 ...
written 2.2 years ago by
Shaun Jackman • 340
0
votes
1
answer
633
views
1
answers
... Hi, Louisa. The default is to load the contigs adjacency file, ecoil100x-6.adj, but your assembly stopped at unitigs, ecoil100x-3.adj. To load the unitigs adjacency file:
Click the arrow to the right of "Stats/Plots" to display "Navigator"
Click the radio button "unitigs"
Click the button "Navi ...
written 2.2 years ago by
Shaun Jackman • 340
Latest awards to Shaun Jackman
Supporter
14 months ago,
voted at least 25 times.
Student
23 months ago,
asked a question with at least 3 up-votes.
For Counting Read Support At A Particular Position Of A Bam File
Popular Question
2.0 years ago,
created a question with more than 1,000 views.
For Counting Read Support At A Particular Position Of A Bam File
Teacher
2.0 years ago,
created an answer with at least 3 up-votes.
For A: Running Abyss On Cluster With Time Limitations
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: Scaffolding with Mate-Pairs Error
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: Scaffolding with Mate-Pairs Error
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Scaffolding with Mate-Pairs Error
Autobiographer
3.4 years ago,
has more than 80 characters in the information field of the user's profile.
Teacher
4.0 years ago,
created an answer with at least 3 up-votes.
For A: Github Workflow For Bioinformatics Analysis
Teacher
4.8 years ago,
created an answer with at least 3 up-votes.
For A: Running Abyss On Cluster With Time Limitations
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