User: cmdcolin

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cmdcolin690
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Bioinformatics at MSU

Posts by cmdcolin

<prev • 144 results • page 1 of 15 • next >
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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 9 days ago by cmdcolin690
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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 16 days ago by cmdcolin690
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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 6 weeks ago by cmdcolin690
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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 10 weeks ago by cmdcolin690
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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 3 months ago by cmdcolin690
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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 3 months ago by cmdcolin690
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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 3 months ago by cmdcolin690
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Ideal settings for blasting a protein/cdna against a genome?
... Are there any ideal settings for BLAST to align a protein or cdna against a genome? Or is it perhaps even misleading to rely on BLAST this way and it's better to use something like exonerate (protein2genome/est2genome)? ...
exonerate blast written 3 months ago by cmdcolin690
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Comment: C: Rename an existing BLAST database
... My particular case the -title argument was also added to the makeblastdb command, and I was hoping to just simply modify the title that was given to the DB rather than regenerate everything with makeblastdb. In this case renaming the files wouldn't work I think since the -title was used. ...
written 3 months ago by cmdcolin690
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Rename an existing BLAST database
... Is it possible to rename an existing BLAST database using the NCBI command line tools? ...
blast written 3 months ago by cmdcolin690 • updated 3 months ago by st.ph.n1.9k

Latest awards to cmdcolin

Appreciated 9 weeks ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Scholar 6 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 6 months ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Centurion 6 months ago, created 100 posts.
Appreciated 7 months ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
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Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 3.0 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Scholar 3.0 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
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