User: Jautis

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Jautis280
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United States
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4 years, 7 months ago
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Posts by Jautis

<prev • 95 results • page 1 of 10 • next >
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Efficiently run blat for long sequences
... Hello, I'm using blat to align genes from one genome to another. This is working well for small sequences (<10kb), but longer sequences are running for an more than a day with no signs of finishing. This seems to be especially true for those 35kb+ and some of the sequences are near 200kb. Does ...
assembly sequence alignment blat written 9 days ago by Jautis280
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Annotate CpG Islands for a new genome
... Hello, we've sequenced a mammalian genome (~3.2gb) and are looking to annotate CpG islands. Ideally, we would get something like the UCSC annotation tracts, but I can't find a public pipeline for doing CpG island calling. Can anyone point me in the right direction? Thank you very much! ...
assembly cpg annotation written 5 months ago by Jautis280 • updated 5 months ago by vkkodali1.2k
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Comment: C: Error in transferring annotations to a new assembly using RATT
... This seems likely, but they don't recommend a version to use. There's also a copy of nucmer within PAGIT I can refer to, but that doesn't change anything either ...
written 8 months ago by Jautis280
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Comment: C: Error in transferring annotations to a new assembly using RATT
... Thank you for the response! Thank you for noting I should export the PATH, but that doesn't resolve the problem. By standalone version, do you mean the one from https://svn.code.sf.net/p/ratt/code/? I just tried that, but it returned the same error message. It sounds like you've been able to mak ...
written 8 months ago by Jautis280
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Error in transferring annotations to a new assembly using RATT
... Hello, I am using RATT to try and transfer gene annotations from a published genome to a new assembly for a sister taxa. However, I am getting an error message (copied below). Following this message, RATT finishes running, but fails to transfer any of the annotations. This error message remains afte ...
software error annotation alignment assembly written 8 months ago by Jautis280 • updated 6 months ago by h.mon27k
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Create a pseudo-haploid fasta file based genotype calls for an individual (vcf file)
... Hi, I have a reference fasta file and a vcf file of SNP variant calls. For each individual in the vcf file, I want to create a new, "pseudo-haploid" fasta file where every base is randomly sampled from one of the individual's alleles. This seems to be a different problem than GATK's FastaAlternate ...
vcf assembly sequence snp written 10 months ago by Jautis280 • updated 10 months ago by Len Trigg1.3k
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Find SNPs which disrupt CpG sites
... Hi, I have a vcf file and I want to find which variants disrupt a CpG site (given by a matching fasta file). I'm sure there is an easy way to do this, but does anyone have any suggestions? I'd settle for a way to annotate the location of each CpG site from the fasta file, which I could then inters ...
vcf genome variants written 10 months ago by Jautis280
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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 13 months ago by Jautis280
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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 13 months ago by Jautis280
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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 13 months ago by Jautis280

Latest awards to Jautis

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 6 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 7 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 Compare tree topologies (Newick)
Popular Question 10 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 13 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 13 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 20 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 20 months ago, created a question with more than 1,000 views. For Taking genotypes out of a vcf file
Popular Question 20 months ago, created a question with more than 1,000 views. For Help simulating RRBS reads
Popular Question 22 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 23 months ago, created a question with more than 1,000 views. For Compare tree topologies (Newick)
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Calling SNPs from RRBS data
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Comparing two phylogenies
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Modifying fasta file based on vcf information
Student 4.0 years ago, asked a question with at least 3 up-votes. For Comparing two phylogenies
Scholar 4.2 years ago, created an answer that has been accepted. For A: SNPs, genotypes, HWE in GWAS,
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Calculating the bisulfite conversion rate
Scholar 4.3 years ago, created an answer that has been accepted. For A: SNPs, genotypes, HWE in GWAS,

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