User: tyler.weirick

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tyler.weirick120
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Posts by tyler.weirick

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Comment: C: Looking for information on designing effective accession numbers.
... Hi Julie, I liked your paper. I am finishing up my own paper and would like to cite yours. Do you have any estimate regarding when it will be published? ...
written 2.9 years ago by tyler.weirick120
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Answer: A: Assembly of transcripts of specific genes from the RNA-seq data
... Why not just use one of the faster pseudo-alignment assemblers?  I have heard good things about Kallisto http://pachterlab.github.io/kallisto/ . Supposedly it is like 1000 times faster than a Tophat+Cufflinks assembly. I think there are a number of other fast assemblers like this https://en.wikipedi ...
written 3.0 years ago by tyler.weirick120
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Looking for information on designing effective accession numbers.
... I am working on a paper that will feature a database with novel lncRNAs. I have searched for several days trying to find information about good design practices for accession numbers. Unfortunalty everything seems to contain the word accession, so I am having difficulty finding material (if it even ...
genome annotation database accession written 3.3 years ago by tyler.weirick120 • updated 3.3 years ago by Sean Davis24k
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How to cite genome assemblies?
... Part of a paper I am writing involves comparing different human genome assemblies. I would like to have some kind of citation for the assemblies hg18, hg19, and hg38. It seems like many other papers do not cite them, for example http://nar.oxfordjournals.org/content/early/2010/10/18/nar.gkq963.full ...
assembly citation written 3.4 years ago by tyler.weirick120 • updated 3.4 years ago by keith130
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Answer: A: Running Pymol From Python Script
... I encountered this problem on Ubuntu 12.04 running pymol verson 1.4.1 (the version installed with apt-get) . I removed that version and reinstalled pymol 1.6.0.0 and was able to get it to work. ...
written 4.7 years ago by tyler.weirick120
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Analyzing Overlap Of Results Between Blast Queries. Is There A Tool For This? If Not What About This Approach?
... I am using various set of enzymes organized into classes in my research. As part of this I use PSI-BLAST to increase the size of my data sets. I known there is a large amount of overlap returned in the results but I would like to get a better view of what is going on exactly. I would prefer not to r ...
visualization blast+ written 5.2 years ago by tyler.weirick120
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Blastclust Has Been Depreciated. Does Anyone Know Why?
... I am working on machine learning project using SVMs. One of the steps in the preparation of my data sets is to reduce the sequence similarity in each class to 40%. I have compared CD-HIT and BLASTCLUST for this step. BLASTCLUST keeps more sequences that CD-HIT. It is tempting to use this data as lar ...
clustering blast+ written 5.2 years ago by tyler.weirick120 • updated 4.0 years ago by Jose Manuel Duarte270
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Does A Script Exist That Given A Species Name Will Give You Kingdom Which The Input Belongs To?
... Does a script exist that given a species name will give you kingdom which the input belongs to? I am doing data analysis on very large sets of blast results and something like this would be a huge help. I am thinking about writing one myself but if something like this exists I would rather not reinv ...
phylogeny taxonomy script written 5.5 years ago by tyler.weirick120 • updated 5.5 years ago by SES8.1k

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Student 9 months ago, asked a question with at least 3 up-votes. For Blastclust Has Been Depreciated. Does Anyone Know Why?
Appreciated 17 months ago, created a post with more than 5 votes. For Blastclust Has Been Depreciated. Does Anyone Know Why?
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Popular Question 4.6 years ago, created a question with more than 1,000 views. For Blastclust Has Been Depreciated. Does Anyone Know Why?
Student 4.6 years ago, asked a question with at least 3 up-votes. For Blastclust Has Been Depreciated. Does Anyone Know Why?

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