User: Chris Fields

gravatar for Chris Fields
Chris Fields1.8k
Reputation:
1,820
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Location:
University of Illinois Urbana-Champaign
Twitter:
cjfields
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Last seen:
11 hours ago
Joined:
7 years, 10 months ago
Email:
c********@gmail.com

I work a lot. I'm very sleepy.

Posts by Chris Fields

<prev • 221 results • page 1 of 23 • next >
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Comment: C: Kraken failing to map reads when reads are merged.
... A few questions: 1) What are the read lengths? 2) What is the expected insert size? You are getting a pretty substantial drop in sequences when merging, which makes me wonder whether those that are merging are in poor quality regions. ...
written 1 day ago by Chris Fields1.8k
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Comment: C: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
... Yes, the DeepVariant paper might be a good candidate for most over-hyped. I was pretty disappointed in it. ...
written 4 weeks ago by Chris Fields1.8k
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News: Community Feedback - OBF mailing list issues
... The Open Bioinformatics Foundation has hosted a number of mail lists for specific Bio* projects like Biopython, BioPerl, Biojava, Bioruby, and EMBOSS. Over the last 3-4 months the mailing lists have been severely hindered due to heavy spam emails to the OBF Mailman instance. We're now actively mig ...
bioperl biopython biojava news emboss bioruby written 4 weeks ago by Chris Fields1.8k
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Answer: A: How to find out the insert size in RNA seq data
... No, that's the run ID, see the [wikipedia article][1]. If you have paired-end reads, you'll need to align them as such for an insert size to be reported. [1]: https://en.wikipedia.org/wiki/FASTQ_format#Illumina_sequence_identifiers ...
written 4 months ago by Chris Fields1.8k
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Comment: C: How to change Bioperl's Bio::SeqIO default sequence folding?
... It's under: ``` perldoc Bio::SeqIO::fasta ``` Look for the `width` function. ...
written 4 months ago by Chris Fields1.8k
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Answer: A: How to change Bioperl's Bio::SeqIO default sequence folding?
... You should be able to set the `width` parameter on the output stream to be what you want: ``` my $out = Bio::SeqIO->new(-file => ">outputfilename" , -width => 100, -format => 'fasta'); ``` I think if this is set to 0, the se ...
written 4 months ago by Chris Fields1.8k
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Answer: A: MACS2 , pvalue
... Tao Liu describes this [on the MACS list in a post][1]. [1]: https://groups.google.com/d/msg/macs-announcement/pBYhN6EBxzc/Dt483n8X3GQJ ...
written 5 months ago by Chris Fields1.8k
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Comment: C: What does 'TLEN' in BAM file mean if mate pairs aligned to different chromosomes
... ...which begs the question on why they report TLEN to begin with in these cases; it seems like that will end up causing someone havoc down the road who doesn't run a sanity check like you have. ...
written 5 months ago by Chris Fields1.8k
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Comment: C: What does 'TLEN' in BAM file mean if mate pairs aligned to different chromosomes
... My guess would be this represent an average of the length for all paired-end reads for this particular fragment, but who knows? This is probably a question best asked of 10x Genomics support, I have found them to be very responsive. ...
written 6 months ago by Chris Fields1.8k
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Comment: C: What does 'TLEN' in BAM file mean if mate pairs aligned to different chromosomes
... One key important part is missing: how was the alignment generated (e.g. tools, parameters, etc)? ...
written 6 months ago by Chris Fields1.8k

Latest awards to Chris Fields

Scholar 4 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Scholar 9 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Commentator 16 months 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 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 18 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Scholar 23 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Guru 2.0 years ago, received more than 100 upvotes.
Centurion 2.2 years ago, created 100 posts.
Scholar 2.2 years ago, created an answer that has been accepted. For A: What is difference between reads and tags?
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
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?
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: What is the difference between GEO and SRA ncbi databases?
Good Answer 2.3 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 2.3 years ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Teacher 2.7 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 3.1 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 3.4 years ago, created an answer that has been accepted. For A: What is the difference between GEO and SRA ncbi databases?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Commentator 3.7 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 3.8 years ago, created a post with more than 5 votes. For A: What is the difference between GEO and SRA ncbi databases?
Scholar 3.8 years ago, created an answer that has been accepted. For A: What is the difference between GEO and SRA ncbi databases?
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Fastq Format Confusion
Voter 3.8 years ago, voted more than 100 times.

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