User: Dave Carlson

gravatar for Dave Carlson
Dave Carlson70
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Location:
Stony Brook University, NY
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1 day, 19 hours ago
Joined:
3 years, 4 months ago
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d*******************@gmail.com

Posts by Dave Carlson

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Help with understanding PAML M0 output
... The free ratio model actually will give you individual dN and dS values for each branch. The output file will have three different trees, one for dS, one for dN, and one of omega. ...
written 4 weeks ago by Dave Carlson70
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Comment: C: How can I use bedtools complement, sam mapping file, and my gtf file to get numb
... Here is the Bedtools intersect documentation. There are a fairly large number of examples provided. https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html ...
written 4 weeks ago by Dave Carlson70
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Comment: C: Help with understanding PAML M0 output
... It's possible I got the model terminology wrong. If you set model = 1 in the control file, this will give you the free-ratio model, which allows each branch to have an independent dN/dS. Looking at the manual again, I see that this different from model M1a, which is a nearly neutral model that is ...
written 5 weeks ago by Dave Carlson70
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Comment: C: Help with understanding PAML M0 output
... N & S are the estimated number of sites in the alignment where a substitution would either be non-synonymous (N) or synonymous (S). This is calculated based on the genetic code and the codon usage model estimated from the data. It is not the same thing as the actual number of synonymous or non ...
written 5 weeks ago by Dave Carlson70
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Answer: A: Assembler for only nanopore data
... I believe Canu is a popular option. Should work for either nanopore or PacBio long read data. ...
written 5 weeks ago by Dave Carlson70
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Answer: A: Help with understanding PAML M0 output
... N and S are the number of non-synonymous and synonymous sites in the alignment, respectively. I believe that t is the length of a particular branch (in substitutions per codon). If you're interested in looking for differences in dN and dS across branches (and not dN/dS, per se) then I believe you ...
written 5 weeks ago by Dave Carlson70
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Comment: C: Randomly select one variant from heterozygous sites in VCF file
... Hi fin swimmer, sorry for the delayed reply. After seeing your question, I realized I wasn't sure what exactly the best option for the output would be. I think maybe turning the heterozygous variant into a homozygous site (either ref or variant) would be good. So in other words,I would like to ...
written 3 months ago by Dave Carlson70
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Randomly select one variant from heterozygous sites in VCF file
... Hi Biostars, Like the title suggests, I have a VCF file and I would like to take every heterozygous position in it and randomly select one of the two alleles to save to a new file. Is there an existing tool that will do this? So far in my searching, I have not found one. Or would I be better off ...
vcf snp written 4 months ago by Dave Carlson70 • updated 4 months ago by finswimmer11k
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Comment: C: What is the -nct alternative in GATK 4.0.0.0?
... Here is what the GATK developers [say][1] about using the HaplotypeCaller Spark implementation: > This tool DOES NOT match the output of HaplotypeCaller. * * It is > still under development and should not be used for production work. * > * For evaluation only. * * Use the non-spark Haploty ...
written 12 months ago by Dave Carlson70
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Comment: C: What is the -nct alternative in GATK 4.0.0.0?
... Fixed, thanks. :) ...
written 12 months ago by Dave Carlson70

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Popular Question 20 days ago, created a question with more than 1,000 views. For codeml jobs taking much longer on a server than on an imac
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
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Popular Question 9 months ago, created a question with more than 1,000 views. For RepeatModeler finishes without creating output files
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?

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