User: Rob Syme

gravatar for Rob Syme
Rob Syme530
Reputation:
530
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Trusted
Location:
Perth, Western Australia
Last seen:
6 months, 3 weeks ago
Joined:
8 years, 11 months ago
Email:
r*******@gmail.com

Working on my PhD, looking at fungal genomics. Am easily excited by fast/cheap sequencing and horizontal gene transfer.

Posts by Rob Syme

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Gatk - Haplotypecaller Is So Slow, What Is Faster And As Good?
... The Fermi paper is also out: http://bioinformatics.oxfordjournals.org/content/28/14/1838 ...
written 3.1 years ago by Rob Syme530
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Comment: C: Filtering fasta file based on identifier
... Maybe /^>\S*P\S*/ To match identifiers (up to the first space) that contain P rather than just identifiers that start with P. ...
written 4.3 years ago by Rob Syme530 • updated 8 months ago by RamRS20k
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Answer: A: Genemark: Can't exec make_mat.v3.0.ini.csh: No such file or directory
... The error is most likely because the c shell (csh) is not installed on your system. If this is the case and you are on Ubuntu, try: sudo apt-get install csh If you have csh installed in a location other than /bin/csh, you will need to change the first line of the make_mat.v3.0.ini.csh script to p ...
written 4.4 years ago by Rob Syme530
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Genemark: Can't exec make_mat.v3.0.ini.csh: No such file or directory
... A common error when running genemark on a fresh Ubuntu install is for gm_es.pl to fail with an error like: Can't exec "/opt/genemark/gmes_bp_linux_64/gmes/make_mat.v3.0.ini.csh": No such file or directory at /opt/genemark/current/gmes/gm_es.pl line 270. The paths may be slightly different, but th ...
annotation genemark maker written 4.4 years ago by Rob Syme530
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Comment: C: ncbi-blast+ ThrowNullPointerException() when running inside a Docker container
... I've upgraded to ubuntu 14.04 (overkill, I know) and upgraded docker to the latest ubuntu docker.io package and everything seems to work ok. Very strange. ...
written 4.7 years ago by Rob Syme530
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ncbi-blast+ ThrowNullPointerException() when running inside a Docker container
... NCBI blast+ seems to have trouble parsing some fasta files when running inside a Docker container. Note that I don't see the error when running blast outside the container. I'm using the sample input file provided by Cegma here as an example, but the problem presists in other files. For the Cegma e ...
ncbi software error cegma blast written 4.7 years ago by Rob Syme530
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Answer: A: Changing To Reverse Complementary Snp Nucleotides
... Maybe some awk: BEGIN{OFS="\t"} function complement (nuc) { switch (nuc) { case /[aA]/: return "T" case /[tT]/: return "A" case /[cC]/: return "G" case /[gG]/: return "C" default: return "N" ...
written 5.5 years ago by Rob Syme530
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Answer: A: Agricultural Chemical Cross Reference
... Most governments will provide a list of agricultural approved chemicals, which will include the active ingredient, its concentration and the trade name of the product. In Australia, the Australian Pesticides and Veterinary Medicines Authority maintains a large database of all approved products. You ...
written 7.1 years ago by Rob Syme530
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Comment: C: Finding An Genomic Intervals Shared For A Given Individual As Called By Two Or M
... One possible solution is the awk command that aaronQuinlan has suggested below. This would split your original file into bed files grouped by the first and fifth column. Is this what you are after? ...
written 7.2 years ago by Rob Syme530
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Answer: A: Finding An Genomic Intervals Shared For A Given Individual As Called By Two Or M
... It sounds like you're looking for bedtools, which allows you to find the intersection of regions (among other things): $ cat algo1.bed chr1 100 1000 chr1 5000 6000 $ cat algo2.bed chr1 150 1200 chr1 7000 8000 $ intersectBed -a algo1.bed -b algo2.bed chr1 150 1000 ...
written 7.2 years ago by Rob Syme530

Latest awards to Rob Syme

Great Question 2.0 years ago, created a question with more than 5,000 views. For Abyss Output File Formats
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Genemark: Can't exec make_mat.v3.0.ini.csh: No such file or directory
Popular Question 3.1 years ago, created a question with more than 1,000 views. For ncbi-blast+ ThrowNullPointerException() when running inside a Docker container
Scholar 4.4 years ago, created an answer that has been accepted. For A: Genemark: Can't exec make_mat.v3.0.ini.csh: No such file or directory
Appreciated 5.5 years ago, created a post with more than 5 votes. For How Do You Identify And Classify Novel Repetitive Elements In A Denovo Genome?
Good Question 5.5 years ago, asked a question that was upvoted at least 5 times. For How Do You Identify And Classify Novel Repetitive Elements In A Denovo Genome?
Good Answer 5.5 years ago, created an answer that was upvoted at least 5 times. For A: Finding An Genomic Intervals Shared For A Given Individual As Called By Two Or M
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Abyss Output File Formats
Popular Question 5.5 years ago, created a question with more than 1,000 views. For How Do You Identify And Classify Novel Repetitive Elements In A Denovo Genome?
Supporter 5.5 years ago, voted at least 25 times.
Commentator 5.5 years ago, created a comment with at least 3 up-votes. For C: What Methods Do You Use For Short Read Mapping?
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Finding An Genomic Intervals Shared For A Given Individual As Called By Two Or M
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Using Ruby To Convert Csv File To Fasta
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Abyss Output File Formats
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Adjacency Files For Abyss-Explorer
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Rearranging Dna Sequences
Student 5.5 years ago, asked a question with at least 3 up-votes. For Abyss Output File Formats
Student 5.5 years ago, asked a question with at least 3 up-votes. For How Do You Identify And Classify Novel Repetitive Elements In A Denovo Genome?
Autobiographer 5.5 years ago, has more than 80 characters in the information field of the user's profile.

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