User: cmdcolin

gravatar for cmdcolin
cmdcolin780
Reputation:
780
Status:
Trusted
Location:
United States
Website:
https://github.com/cmd...
Last seen:
1 week, 1 day ago
Joined:
5 years, 8 months ago
Email:
c**********@gmail.com

Computer Science MS student at Wayne State University

 

Past:

 

Computer Science BS at University of Colorado
Research assistant at University of Missouri
Research assistant at Michigan State University

Posts by cmdcolin

<prev • 147 results • page 1 of 15 • next >
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Answer: A: Interesting/useful/beautiful bio sequence viz tools
... I think that the plugin and customization system of jbrowse allows you to make tons of things that are pretty cool, but having developed for them I'm sort of biased. Anyways, here are some examples of customized tracks in jbrowse made via plugins multiple sequence alignment viewer https://github.co ...
written 3 months ago by cmdcolin780
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Comment: C: bedtools getfasta chromosome not found
... alternative command line fix: use the dos2unix command (dos2unix yourfile.fa) ...
written 3 months ago by cmdcolin780
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Answer: C: Samtools faidx problem
... Shouldn't it be "samtools faidx scaffold.fasta scaffoldX:111614-111868"? ...
written 5 months ago by cmdcolin780
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Answer: A: Add gene annotation/information to CNV plot in R
... In some cases converting your data to a genome browser and then screenshotting the genome browser can be beneficial for getting such genomic contexts. The embedded link also recommends something called genomegraphs also which helps for R graphics A final alternative you could look into is adding a ...
written 7 months ago by cmdcolin780
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Comment: C: Universal Operon Database
... I think the comment implies there may not be (or they may be very rare) operons in human in the classical sense, e.g. where they are polycistronic (multiple transcripts being transcribed at once, and then spliced into different genes after transcription). Uniquely though, c.elegans does have many po ...
written 7 months ago by cmdcolin780
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Comment: C: Scafolding and gap filling
... You can possibly use a "reference based scaffolder" such as medusa, ragout, or other tools. This compares a genome to a closely related one and uses synteny to infer scaffolding ...
written 8 months ago by cmdcolin780
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Comment: C: Rescaffolding a genome assembly?
... I wasn't able to do a really comprehensive comparison of all options but the "rescaffolding" option via running SSPACE using mate pair reads on the broken up contigs produced some new scaffolds that suggested a different arrangement of contigs (it stiched together contigs that were on different scaf ...
written 9 months ago by cmdcolin780
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Comment: C: Repeatmasker, Can't locate Text/Soundex.pm
... Have you tried installing repeatmasker using a simple package manager such as homebrew? `brew install homebrew/science/repeatmasker` works quite well on OSX for me ...
written 10 months ago by cmdcolin780
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Comment: C: Blast Xml For Multiple Databases
... It is definitely possible to do this without aliastool, as mentioned above, passing multiple arguments for db. It has the annoying consequence of not telling you "which" database a particular sequence came from though ...
written 10 months ago by cmdcolin780
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Comment: C: Ideal settings for blasting a protein/cdna against a genome?
... It would be same species or fairly closely related (e.g. getting a danio gene, blasting against fish of interest). I don't necessarily have exact use cases but there were biologists wanting to find the location of their gene of interest in a poorly annotated genome, and they had cdna sequences from ...
written 10 months ago by cmdcolin780

Latest awards to cmdcolin

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Filter VCF by sample?
Appreciated 9 months ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Scholar 13 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 13 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Centurion 13 months ago, created 100 posts.
Appreciated 14 months ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Voter 18 months ago, voted more than 100 times.
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 3.5 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Scholar 3.6 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Supporter 3.7 years ago, voted at least 25 times.
Autobiographer 3.9 years ago, has more than 80 characters in the information field of the user's profile.

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