User: Shaun Jackman

gravatar for Shaun Jackman
Shaun Jackman420
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

<prev • 44 results • page 1 of 5 • next >
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Answer: A: GFF to TBL file conversion for annotation submission
... NCBI now accepts annotations submitted in GFF3 format. See https://www.ncbi.nlm.nih.gov/genbank/genomes_gff/ ...
written 22 days ago by Shaun Jackman420
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Answer: A: "brew install brewsci/bio/abyss" doesn't work - no formula
... 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 Jackman420
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Comment: C: How To Pull Out Qual From Multi Line Fastq?
... 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 Jackman420
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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 9 months ago by Shaun Jackman420
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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 Jackman420
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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 18 months ago by Shaun Jackman420
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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 3.2 years ago by Shaun Jackman420
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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 3.3 years ago by Shaun Jackman420
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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 3.3 years ago by Shaun Jackman420
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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 3.3 years ago by Shaun Jackman420

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
Scholar 9 months ago, created an answer that has been accepted. For A: Abyss genome assembly input
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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