User: Shaun Jackman

gravatar for Shaun Jackman
Shaun Jackman390
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

<prev • 41 results • page 1 of 5 • next >
4
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Answer: A: Assembly with mate-pairs issue
... 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 Jackman390
0
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1
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851
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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 3 months ago by Shaun Jackman390
0
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3
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7.2k
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3
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Comment: C: How to sort a VCF file lexicographically by chromosome number?
... 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 Jackman390
1
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2
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2.5k
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2
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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 2.7 years ago by Shaun Jackman390
4
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2
answers
777
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2
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Answer: A: degenerate nucleotide in abyss assemblies?
... 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 Jackman390
2
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1
answer
907
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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 2.8 years ago by Shaun Jackman390
2
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1
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1.4k
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1
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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 Jackman390
0
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2
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835
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2
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Answer: A: Abyss stuck for past 48 days in generating adjency
... 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 Jackman390
0
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0
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741
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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 2.9 years ago by Shaun Jackman390
0
votes
1
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1.2k
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1
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Comment: C: Scaffolding with Mate-Pairs Error
... Happy to help. Watch that white space! =) ...
written 2.9 years ago by Shaun Jackman390

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
Scholar 3 months ago, created an answer that has been accepted. For A: Abyss genome assembly input
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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