User: Chris Fields

gravatar for Chris Fields
Chris Fields1.8k
Reputation:
1,760
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Location:
University of Illinois Urbana-Champaign
Last seen:
13 hours ago
Joined:
7 years, 6 months ago
Email:
c********@gmail.com

I work a lot. I'm very sleepy.

Posts by Chris Fields

<prev • 218 results • page 1 of 22 • next >
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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 21 days 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 27 days 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 27 days 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 7 weeks 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 8 weeks 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 10 weeks 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 10 weeks ago by Chris Fields1.8k
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Comment: C: genome assembly, larger genome size than expect
... What do the basic overall stats look like when comparing the two assemblies, NG50 for example? I suggest using an arbitrarily high est. genome size when calculating these (maybe 1-1.2Gb) just for comparison purposes, the N50 will not be directly comparable. Also, I recommend looking at MEGAHIT ove ...
written 12 weeks ago by Chris Fields1.8k
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Answer: A: genome assembly, larger genome size than expect
... I have seen this in particularly heterozygous genome assemblies, where you may have alternative haplotypes assembled (though this also rends to shatter the genome assembly by breaking up the graph). It's also possible the genome size is underestimated. Have you run a [kmer abundance analysis][1] o ...
written 3 months ago by Chris Fields1.8k
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Comment: C: STAR mapped more reads to transcriptome
... It's hard to say w/o knowing specifically how you ran STAR. Maybe a difference in the total # of alignments (which may filter more reads in the genome alignment vs transcriptome)? ...
written 3 months ago by Chris Fields1.8k

Latest awards to Chris Fields

Scholar 27 days ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Scholar 5 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Commentator 12 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 14 months ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Scholar 14 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Scholar 19 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
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Scholar 22 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Scholar 22 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Appreciated 24 months ago, created a post with more than 5 votes. For A: What is the difference between GEO and SRA ncbi databases?
Good Answer 24 months ago, created an answer that was upvoted at least 5 times. For A: What is the difference between GEO and SRA ncbi databases?
Scholar 24 months ago, created an answer that has been accepted. For A: What is difference between reads and tags?
Teacher 2.4 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 2.8 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 3.1 years ago, created an answer that has been accepted. For A: What is the difference between GEO and SRA ncbi databases?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Bioperl Has Different Behaviours In Parsing Blast And Blast+ Result
Commentator 3.4 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 3.4 years ago, created a post with more than 5 votes. 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 3.4 years ago, created an answer with at least 3 up-votes. For A: Fastq Format Confusion
Voter 3.5 years ago, voted more than 100 times.

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