User: Shaun Jackman
Shaun Jackman • 390
- Reputation:
- 390
- Status:
- Trusted
- Location:
- Vancouver, Canada
- Website:
- http://sjackman.ca/
- Twitter:
- @sjackman
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 months ago
- Joined:
- 5 years, 10 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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4
votes
1
answer
851
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 3 months ago by
Shaun Jackman • 390
0
votes
1
answer
851
views
1
answers
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 3 months ago by
Shaun Jackman • 390
0
votes
3
answers
7.2k
views
3
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 12 months ago by
Shaun Jackman • 390
1
vote
2
answers
2.5k
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 2.7 years ago by
Shaun Jackman • 390
4
votes
2
answers
777
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 2.8 years ago by
Shaun Jackman • 390
2
votes
1
answer
907
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 2.8 years ago by
Shaun Jackman • 390
2
votes
1
answer
1.4k
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 2.8 years ago by
Shaun Jackman • 390
0
votes
2
answers
835
views
2
answers
... 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 2.8 years ago by
Shaun Jackman • 390
0
votes
0
answers
741
views
0
answers
Comment:
C: Abyss 1.5.2: MergePaths failed
... Please post a gist of these two files:
snow-4.adj snow-4.path1
...
written 2.9 years ago by
Shaun Jackman • 390
0
votes
1
answer
1.2k
views
1
answers
Comment:
C: Scaffolding with Mate-Pairs Error
... Happy to help. Watch that white space! =)
...
written 2.9 years ago by
Shaun Jackman • 390
Latest awards to Shaun Jackman
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Running Abyss On Cluster With Time Limitations
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Github Workflow For Bioinformatics Analysis
Supporter
23 months ago,
voted at least 25 times.
Student
2.7 years ago,
asked a question with at least 3 up-votes.
For Counting Read Support At A Particular Position Of A Bam File
Teacher
2.8 years ago,
created an answer with at least 3 up-votes.
For A: Running Abyss On Cluster With Time Limitations
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Counting Read Support At A Particular Position Of A Bam File
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: Scaffolding with Mate-Pairs Error
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: Scaffolding with Mate-Pairs Error
Scholar
2.9 years ago,
created an answer that has been accepted.
For A: Scaffolding with Mate-Pairs Error
Autobiographer
4.1 years ago,
has more than 80 characters in the information field of the user's profile.
Teacher
4.7 years ago,
created an answer with at least 3 up-votes.
For A: Github Workflow For Bioinformatics Analysis
Teacher
5.6 years ago,
created an answer with at least 3 up-votes.
For A: Running Abyss On Cluster With Time Limitations
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