User: Shaun Jackman

gravatar for Shaun Jackman
Shaun Jackman340
Reputation:
340
Status:
Trusted
Location:
Vancouver, Canada
Website:
http://sjackman.ca/
Twitter:
@sjackman
Scholar ID:
Google Scholar Page
Last seen:
6 months ago
Joined:
5 years, 5 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 • 39 results • page 1 of 4 • next >
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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 6 months ago by Shaun Jackman340
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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 2.3 years ago by Shaun Jackman340
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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 2.4 years ago by Shaun Jackman340
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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 2.4 years ago by Shaun Jackman340
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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 2.4 years ago by Shaun Jackman340
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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 2.4 years ago by Shaun Jackman340
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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 2.5 years ago by Shaun Jackman340
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Comment: C: Scaffolding with Mate-Pairs Error
... Happy to help. Watch that white space! =) ...
written 2.5 years ago by Shaun Jackman340
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Answer: A: Scaffolding with Mate-Pairs Error
... 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 2.5 years ago by Shaun Jackman340
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Answer: A: ABySS-Explorer cannot find my adj file
... 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 2.5 years ago by Shaun Jackman340

Latest awards to Shaun Jackman

Supporter 17 months ago, voted at least 25 times.
Student 2.3 years ago, asked a question with at least 3 up-votes. For Counting Read Support At A Particular Position Of A Bam File
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Counting Read Support At A Particular Position Of A Bam File
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Running Abyss On Cluster With Time Limitations
Scholar 2.4 years ago, created an answer that has been accepted. For A: Scaffolding with Mate-Pairs Error
Scholar 2.4 years ago, created an answer that has been accepted. For A: Scaffolding with Mate-Pairs Error
Scholar 2.5 years ago, created an answer that has been accepted. For A: Scaffolding with Mate-Pairs Error
Autobiographer 3.7 years ago, has more than 80 characters in the information field of the user's profile.
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Github Workflow For Bioinformatics Analysis
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Running Abyss On Cluster With Time Limitations

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