User: Chris Fields

gravatar for Chris Fields
Chris Fields2.1k
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University of Illinois Urbana-Champaign
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cjfields
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I work a lot. I'm very sleepy.

Posts by Chris Fields

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News: Call for Abstracts: BOSC 2019: Bioinformatics Open Source Conference
... ![BOSC_2019_Banner][1] ## BOSC 2019: Bioinformatics Open Source Conference ### An ISMB/ECCB Community of Special Interest (COSI) **BOSC 2019 Dates**: July 24-25, 2019 **Location**: Basel, Switzerland **Website**: https://www.open-bio.org/wiki/BOSC_2019 (new, improved website coming soon!) ** ...
conference news open source bosc written 4 months ago by Chris Fields2.1k
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Answer: A: subset sample in phyloseq
... You should read the `phyloseq` documentation for this, there are a ton of examples for subsetting or pruning data. Also: https://joey711.github.io/phyloseq/preprocess.html More specifically, look up the online documentation in R for `subset_samples`, `prune_samples`, `subset_taxa`, and `prune_tax ...
written 4 months ago by Chris Fields2.1k
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Answer: A: Algal vs bacterial 16s chloroplast
... This depends on how different the 16S from Chlamydomonas is from cyanos (and whether you can detect this from the V4 region alone). Do you see any other cyano sequences popping up beside the one ASV with the chloroplast assignment? ...
written 4 months ago by Chris Fields2.1k
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News: Course on Programming for Evolutionary Biology
... Course on Programming for Evolutionary Biology When: March 12th - March 28th 2019 Location: Berlin, Germany, at the Free University of Berlin. Application deadline: December 31st 2018 Detailed information about the course content and how to apply: http://evop.bioinf.uni-leipzig.de/ In this in ...
genome python news evolution R written 7 months ago by Chris Fields2.1k
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Comment: C: GCCBOSC 2018: A Bioinformatics Community Conference Call for Abstracts
... Here they are, just recently posted by https://www.biostars.org/u/743/ and Co.: https://galaxyproject.org/news/2018-11-gccbosc-videos/ ...
written 7 months ago by Chris Fields2.1k
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Comment: C: How to recover a 16S rRNA gene from genome reads?
... I should add, I've also started looking into [phyloFlash][1] for this, which can use SortMeRNA 'under the hood'. Seems very nice. [1]: https://github.com/HRGV/phyloFlash ...
written 7 months ago by Chris Fields2.1k
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Comment: C: De novo assembly programm
... Hey, if it works well enough for your needs then I think that's fine. We've had SPAdes killed for using too much memory on a number of genome assemblies in the 200-800MB range (we have a 1TB assembly node and access to a 3TB if needed), and the assemblies that do finish take forever and are less id ...
written 12 months ago by Chris Fields2.1k
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Comment: C: De novo assembly programm
... Note that SPAdes is primarily developed for small genomes; it tends to use a lot of memory, and I have found it impossible to use for many assemblies above 200-300Mb. Have you tried [Platanus][1]? I believe this worked for past butterfly genomes and can handle highly heterozygous genomes. You c ...
written 12 months ago by Chris Fields2.1k
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Comment: C: De novo assembly programm
... I would add to this: have you checked the overall kmer abundance distribution, to see whether the sample is heterozygous, coverage is as expected, etc? Jellyfish + GenomeScope are useful here. Similarly preQC worked well for us in identifying problematic assemblies, which can do a bit of the above ...
written 13 months ago by Chris Fields2.1k
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Answer: A: BUSCO producing different genome completeness
... This is expected; different taxonomic groups would have different single-copy orthologs (with more refined taxonomic groups having more SCOs compared to broader groups). Also, I know several nematode genomes have lower than expected BUSCO scores, which may be due to issues with assembly, etc. ...
written 13 months ago by Chris Fields2.1k

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Scholar 4 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Scholar 18 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Scholar 23 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Scholar 2.3 years ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Bwa mem is exiting with segmentation fault for large contigs (> 0.4Mbp)
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Scholar 3.0 years ago, created an answer that has been accepted. For A: What is difference between reads and tags?
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Scholar 3.7 years ago, created an answer that has been accepted. For A: What is difference between reads and tags?
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