User: Chris Fields

gravatar for Chris Fields
Chris Fields1.9k
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1,950
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Location:
University of Illinois Urbana-Champaign
Twitter:
cjfields
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Last seen:
1 day, 22 hours ago
Joined:
8 years, 6 months ago
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I work a lot. I'm very sleepy.

Posts by Chris Fields

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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 11 weeks ago by Chris Fields1.9k
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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 11 weeks ago by Chris Fields1.9k
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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 12 weeks ago by Chris Fields1.9k
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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 3 months ago by Chris Fields1.9k
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Comment: C: Getting GI number from NCBI database through code
... I normally don't post replies to homework or project-based questions, but I'll simply point to this post (and indicate you should point this out to your course instructor, it's been two years since the original announcement): https://www.ncbi.nlm.nih.gov/books/NBK431010/#news_03-02-2016-phase-out ...
written 4 months ago by Chris Fields1.9k
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Answer: A: Problem with MACS2 results
... The error is a hint. A certain number of reliable peaks have to be called for the shift model building step (I think this is ~1-10k). For a smaller genome like *M. xanthus* this may be an issue as I don't think it's directly adjustable, but you can try adjusting the MFOLD parameter to get more pea ...
written 4 months ago by Chris Fields1.9k
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Job: Visiting Research Specialist in Life Science - University of Illinois Urbana-Champaign
... The Roy J. Carver Biotechnology Center has an opening for a Visiting Research Specialist in Life Science in HPCBio. The primary function of the position is to process and analyze 'omics data produced by customers of the HPCBio group. This position is a one year commitment with the potential for rene ...
assembly python chip-seq job R rna-seq written 5 months ago by Chris Fields1.9k
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Comment: C: Anyone knows how to create a figure like this?
... Of course, but it seems this seldom happens. I'm guessing it's b/c doing so requires the submitter to request this of a moderator? ...
written 5 months ago by Chris Fields1.9k
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Comment: A: Anyone knows how to create a figure like this?
... It's not a 2D plot, it's 3D. Maybe try plots allowing 3 axes including categorical data? **EDIT**: nevermind, I see that a link was added above by https://www.biostars.org/u/25721/. We really need a way to promote in-line replies as the answer. ...
written 5 months ago by Chris Fields1.9k
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Comment: C: How to best upload bam files in R for analysis of alternative splicing
... The question to me appears to be asking how to upload BAMs into R, not what packages in R are others using for alternative splicing. ...
written 6 months ago by Chris Fields1.9k

Latest awards to Chris Fields

Scholar 7 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Scholar 12 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Scholar 17 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Commentator 2.0 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 2.2 years ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Scholar 2.2 years ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Scholar 2.6 years ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Guru 2.7 years ago, received more than 100 upvotes.
Centurion 2.8 years ago, created 100 posts.
Scholar 2.8 years ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Scholar 2.8 years ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: What is the difference between GEO and SRA ncbi databases?
Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For A: What is the difference between GEO and SRA ncbi databases?
Scholar 3.0 years ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Good Answer 3.8 years ago, created an answer that was upvoted at least 5 times. For A: What is the difference between GEO and SRA ncbi databases?
Scholar 4.1 years ago, created an answer that has been accepted. For A: What is the difference between GEO and SRA ncbi databases?
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Commentator 4.4 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)
Appreciated 4.4 years ago, created a post with more than 5 votes. For A: What is the difference between GEO and SRA ncbi databases?
Scholar 4.4 years ago, created an answer that has been accepted. For A: What is the difference between GEO and SRA ncbi databases?

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