User: Jautis

gravatar for Jautis
Jautis260
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260
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United States
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1 month ago
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3 years, 8 months ago
Email:
t***@duke.edu

Posts by Jautis

<prev • 88 results • page 1 of 9 • next >
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Determine the derived allele
... Hi, I'm working in a non-model primate and we have an assembled genome comprised of various scaffolds. We sequenced a population of individuals and would like to determine which is the derived vs ancestral allele. Conceptually, this is simply using an outgroup (in this case, the best choice is the ...
alignment written 9 weeks ago by Jautis260
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Comment: C: GOseq with non-supported organism
... We're working with the anubis baboon (genome Panu2.0). But thank you! I hadn't seen the biomaRt annotation tools ...
written 11 weeks ago by Jautis260
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GOseq with non-supported organism
... Hi, I want to do GO analsis on a set of differentially methylated genes (I have the ENSEMBL identifier for each gene). I did an initial analysis using ClueGO (implemented within Cytoscape), but want to do a followup using GOseq (the R package). This is because different number of CpG sites/tests per ...
R goseq go written 11 weeks ago by Jautis260
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Comment: C: Find chromosomal location of a scaffold
... Thanks for the clarification! ...
written 12 weeks ago by Jautis260
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Comment: C: Find chromosomal location of a scaffold
... Thanks for the response. However, the answer and methods you refer me to have to do with mapping reads to a genome. What I'm interested in doing is aligning fasta genomes to each other (or rather, finding the chromosome location scaffold X corresponds with). ...
written 12 weeks ago by Jautis260
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Find chromosomal location of a scaffold
... For two closely related species, is there an easy way to align genome assemblies? Species A is a chromosomal assembly (although it has gaps) and Species B is assembled into smaller scaffolds. I would like to figure out where Species B scaffolds lie on the Species A assembly in order to leverage an ...
genome mapping written 12 weeks ago by Jautis260 • updated 12 weeks ago by h.mon20k
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Comment: C: Convert an altered sam file into a bam file
... Thanks! I went ahead and added the first 25 lines to the initial question. Yes, I am keeping the same header that I initially generated. I am adding additional fields (NM, MD, XM, XR, and XG flags with dummy values) ...
written 10 months ago by Jautis260
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Convert an altered sam file into a bam file
... Hi, I have a sam file from BSMap which I have modified into the format of a sam file from bismark. However, after doing so, I'm no longer able to convert the sam file into a bam file using samtools. What is it that I'm missing? The more general version of this question would be when are you able t ...
bam sam sequencing written 10 months ago by Jautis260
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BSMap to Bismark bam file formats
... Hi, I'm wondering how to go about transforming a file between different bam formats. In particular, I am interested in switching a file mapped with BSMap into the Bismark bam file format for downstream analyses. I want to do so because BSMap, from simulations I've run, maps heterospecific reads with ...
sequencing next-gen bisulfite bam written 10 months ago by Jautis260
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Comment: C: Genotype calls for a list of variable sites
... That's useful, but is there a way to always call the sites, even if there isn't enough information to identify a variable site in the new dataset? ...
written 12 months ago by Jautis260

Latest awards to Jautis

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 9 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 9 months ago, created a question with more than 1,000 views. For Taking genotypes out of a vcf file
Popular Question 9 months ago, created a question with more than 1,000 views. For Help simulating RRBS reads
Popular Question 11 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 12 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 15 months ago, created a question with more than 1,000 views. For Calling SNPs from RRBS data
Popular Question 17 months ago, created a question with more than 1,000 views. For Comparing two phylogenies
Popular Question 23 months ago, created a question with more than 1,000 views. For Modifying fasta file based on vcf information
Student 3.1 years ago, asked a question with at least 3 up-votes. For Comparing two phylogenies
Scholar 3.3 years ago, created an answer that has been accepted. For A: SNPs, genotypes, HWE in GWAS,
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Calculating the bisulfite conversion rate
Scholar 3.4 years ago, created an answer that has been accepted. For A: SNPs, genotypes, HWE in GWAS,

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