Moderator: SES

gravatar for SES
SES7.8k
Reputation:
7,850
Status:
Trusted
Location:
Vancouver, BC
Website:
http://uga.academia.ed...
Scholar ID:
Google Scholar Page
Last seen:
4 weeks ago
Joined:
5 years, 2 months ago
Email:
s*******@gmail.com

I have a PhD in Genetics and my primary research focus is on mechanisms of genome evolution involving transposable elements. I also work on many other projects related to genome assembly, annotation, and gene family evolution. 


Here are some of the bioinformatics projects I've developed:


Websites I have developed and maintain:

Posts by SES

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Comment: C: R install error
... Hello jolin0701-dy! We believe that this post does not fit the main topic of this site. Not a bioinformatics question. Search the error online, that is a much faster approach. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community c ...
written 11 weeks ago by SES7.8k
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Comment: C: JGI's Taxonomy Server
... There is a well-documented NCBI webservice called [E-utilities](https://www.ncbi.nlm.nih.gov/books/NBK25501/) that already handles all of this for you. You form a standard request and parse the response with something like libxml. It is therefore trivial to get text output with a shell command or a ...
written 12 weeks ago by SES7.8k
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Comment: C: JGI's Taxonomy Server
... It's not completely clear why one would use this service. Perhaps you could clarify a few things. Is this getting data directly from NCBI through the taxonomy browser or the E-Utilities webservice? If so, why would you not want to use NCBI directly? Is the overall goal just to get JSON/text formats, ...
written 12 weeks ago by SES7.8k
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Answer: A: How to extract specific columns based on a set of different header patterns in a
... You are very close and I appreciate the effort. I'll share the thing you are missing and some other helpful tips because you basically have all the logic right. (I personally think it would be better to use vcf-tools or one of the associated VCF modules to work on the indexed files more efficiently. ...
written 4 months ago by SES7.8k
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Answer: A: uneven paired end reads in bowtie
... Instead of doing the trimming again (which can be a long process), the easiest solution is to repair the reads. Here's a very lightweight solution for pairing the reads (using [Pairfq](https://github.com/sestaton/Pairfq/wiki)): curl -sL git.io/pairfq_lite | perl - makepairs -f R1_trim.fq.gz -r ...
written 4 months ago by SES7.8k
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Comment: C: Ensembl Perl API
... I'm not certain this is the only issue, but you spelled "thaliana" wrong. Also, I recommend following best practices and putting 'use strict;' and 'use warnings;' in your script. That will make debugging so much easier. ...
written 5 months ago by SES7.8k
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Comment: C: bio::db::sam installation error
... If you want to try Bio::DB::HTS, fetch the latest release, then do the normal `configure` and `make` followed by `export HTSLIB_DIR=path` where "path" is the source distribution. Then you can do `cpanm Bio::DB::HTS` with no problem. If you are using code that already exists then stick to Bio::DB::S ...
written 7 months ago by SES7.8k
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Comment: C: bio::db::sam installation error
... Aside from the version issue, you probably only installed the `samtools` binary and the Perl module needs the library files to compile against. So, I'm certain this won't work because there is possibly no library available and it would be the wrong version if it could be found. ...
written 7 months ago by SES7.8k
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Answer: A: bio::db::sam installation error
... To save some space, I'll just point you to [StackOverflow](http://stackoverflow.com/a/25611671/1543853) where I've answered this a couple of times. It is important that you compile samtools correctly, make sure it can be found by the Perl module, and use a version that the Perl module was designed t ...
written 7 months ago by SES7.8k
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Comment: C: NCBI MagicBlast ( Short read mapper )
... > The input reads may be provided as SRA accession or file in a SRA, FASTA, FASTQ, or FASTC format. Read pairs can be presented as parallel files, or as successive reads in a single file. That will save SO much time to take SRA files or accessions directly. Also, what is FASTC? All I can find is ...
written 7 months ago by SES7.8k

Latest awards to SES

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Need Help Interpreting A Qtl Plot In A Merge Analysis
Scholar 4 months ago, created an answer that has been accepted. For A: Transposable element classification
Scholar 7 months ago, created an answer that has been accepted. For A: Transposable element classification
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Need Help Interpreting A Qtl Plot In A Merge Analysis
Scholar 8 months ago, created an answer that has been accepted. For A: Transposable element classification
Scholar 8 months ago, created an answer that has been accepted. For A: Transposable element classification
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Simple Tool For Finding Known Regulatory Motifs In A Single (Eukaryotic) Sequenc
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Need Help Interpreting A Qtl Plot In A Merge Analysis
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Need Help Interpreting A Qtl Plot In A Merge Analysis
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Need Help Interpreting A Qtl Plot In A Merge Analysis
Appreciated 10 months ago, created a post with more than 5 votes. For A: How To Split A Long Dna Sequence Into Certain Length Parts By Perl/Python ?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Need Help Interpreting A Qtl Plot In A Merge Analysis
Scholar 11 months ago, created an answer that has been accepted. For A: Transposable element classification
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Need Help Interpreting A Qtl Plot In A Merge Analysis
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Need Help Interpreting A Qtl Plot In A Merge Analysis
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Need Help Interpreting A Qtl Plot In A Merge Analysis
Popular Question 15 months ago, created a question with more than 1,000 views. For What Are Some Tools/Methods For Identifying Microhomology Between Short Sequences?
Scholar 17 months ago, created an answer that has been accepted. For A: Transposable element classification
Appreciated 17 months ago, created a post with more than 5 votes. For C: Biopython or Bioperl help
Scholar 17 months ago, created an answer that has been accepted. For A: Transposable element classification
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Need Help Interpreting A Qtl Plot In A Merge Analysis

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