User: cmdcolin

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cmdcolin640
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640
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Bioinformatics at MSU

Posts by cmdcolin

<prev • 134 results • page 1 of 14 • next >
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Answer: A: List of np-hard problems in biology/bioinformatics
... Scaffolding as well as de novo assembly are formally NP hard but have many heuristics "The prevalence of heuristic choices in assembly owes its origins partly to several well-known early results regarding its computational complexity [1, 2] (and further confirmed by recent studies [3, 4]) which sug ...
written 11 days ago by cmdcolin640
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Comment: C: What is the difference between GTF AND GFF format
... The second link had weird formatting, here is the correct one for "2.2" http://mblab.wustl.edu/GTF22.html ...
written 13 days ago by cmdcolin640
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Comment: C: PERL: How I can "save information in a hash (%)"?
... Not to beat a dead horse, but if it is an assignment, it does not appear to say "use bioperl". You may find it better to use the perl by itself first before resorting to bioperl ...
written 20 days ago by cmdcolin640
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Comment: C: How to correctly use E-fetch from E-utilities?
... One nice way of installing eutils is to use Homebrew (http://brew.sh) or Linuxbrew (http://linuxbrew.sh). Then you can run `brew install homebrew/science/edirect` ...
written 27 days ago by cmdcolin640
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Answer: A: [E::hts_idx_push] chromosome blocks not continuous :Indexing of gff3 files using
... I believe it would just be "sort -k1,1" and not "sort -k1,1n". also when using genometools you need to use -sortlines, not just -sort Depending on your usage of the tabix gff3, you might also consider this method http://biorxiv.org/content/early/2017/06/04/145938 which is important for jbrowse ...
written 4 weeks ago by cmdcolin640
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Comment: C: Ucsc/Ensembl Bam Converter?
... it would be great if there was a toolkit for ID conversions like this ...
written 4 weeks ago by cmdcolin640
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Answer: A: retrieve genomic coordinate on mRNA
... Tools like Ensembl VEP can do this, and will output things like cDNA position and CDS position (e.g. with or without counting the UTR) The https://mutalyzer.nl/ tool also looks interesting These may not be the most lightweight or purpose built, and only may work on certain organisms I think the ...
written 4 weeks ago by cmdcolin640
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Answer: A: Efficient And Fastest Way To Sort Large (>100Gb) Bam Files?
... One more option by DNANexus that tries to obtain a speedup by using a RocksDB backend (trying to improve file I/O from what I can gather) http://devblog.dnanexus.com/faster-bam-sorting-with-samtools-and-rocksdb/ uses a fork of samtools on github ...
written 5 weeks ago by cmdcolin640
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Comment: C: Teaching a course on RESTful microservices; looking for example projects
... Is there any particular reason that the target app is a pipeline? Microservices seem to me to shine as part of a web application e.g. a bioinformatics database. Just seems to me a more obvious use of "microservices" is to stand as pieces of "middleware" between the "data" (whether that is an actual ...
written 5 weeks ago by cmdcolin640
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Comment: C: How large are 1000genomes vcf files?
... You can also gzip your output... ...
written 5 weeks ago by cmdcolin640

Latest awards to cmdcolin

Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 11 weeks ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Centurion 12 weeks ago, created 100 posts.
Appreciated 3 months ago, created a post with more than 5 votes. For C: StackExchange/Area51 bioinformatics is back
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Voter 7 months ago, voted more than 100 times.
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 2.6 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Scholar 2.7 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Supporter 2.8 years ago, voted at least 25 times.
Autobiographer 3.0 years ago, has more than 80 characters in the information field of the user's profile.

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