User: Ahdf-Lell-Kocks

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Ahdf-Lell-Kocks1.6k
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Posts by Ahdf-Lell-Kocks

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Comment: C: Tools For De Novo Assembly Of Mirnas?
... Thanks, very useful comments. I did try Trinity's clustering step, and it does find a bunch of clusters of 10-15 36bp reads with an offset of 1bp, but according to what you say, these shouldn't be mature miRNAs, right? ...
written 7.0 years ago by Ahdf-Lell-Kocks1.6k
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Answer: A: Mapping Orthologs On Fasta Files
... If what you mean is that you want to visualise your orthology relationships to the genomic fasta file, you can generate a GFF file from your list of orthologs and then visualize it with a program like IGV or similar. ...
written 7.0 years ago by Ahdf-Lell-Kocks1.6k
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Answer: A: Phylogenetic Tree Read And Interprettion
... The bootstrap values signify how sure one can be that the tree is correct at any given node. A tree is calculated by looking at existing molecular data, and the more data one can gather, the easier it will be to relate the sequences in a highly-confident phylogeny. If the sequence evidence is not go ...
written 7.1 years ago by Ahdf-Lell-Kocks1.6k
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Comment: C: Low Support Value Of Phylogenetic Trees
... The bootstrap values signify how sure one can be that the tree is correct at any given node. A tree is calculated by looking at existing molecular data, and the more data one can gather, the easier it will be to relate the sequences in a highly-confident phylogeny. If the sequence evidence is not go ...
written 7.1 years ago by Ahdf-Lell-Kocks1.6k
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Answer: A: Mapping Reads Back To Assembly Contigs
... There is one main consideration in trying to reproduce the coverage profile from an assembly of short reads: You do it during assembly without using information, or You do it post-assembly, possibly losing information. Most assemblers for NGS data won't do it by default during assembly since it ...
written 7.1 years ago by Ahdf-Lell-Kocks1.6k
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Tools To Identify Compound Heterozygous Variants?
... Are there any tools to identify compound heterozygous variants in resequencing data? By compound heterozygosity I mean a catalog of multiple deleterious mutations (PolyPhen? or SIFT?) that happen to fall as hets into different locations of the same genes. ...
software written 7.1 years ago by Ahdf-Lell-Kocks1.6k • updated 5.0 years ago by mans.magnusson10
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Answer: A: How To Compare Two Proteome Sets At 30% Similarity?
... I would try jackhmmer from the HMMER 3.0 package. Something like: ~/hmmer3.0/jackhmmer proteome1.fasta proteome2.fasta ...
written 7.1 years ago by Ahdf-Lell-Kocks1.6k
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Comment: C: Common Viral Dna In Human Sequencing Samples?
... thanks. hasn't anybody done such query on SRA samples that has the answer? ...
written 7.1 years ago by Ahdf-Lell-Kocks1.6k
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Eqtl Data In Dogs?
... Is there any publicly available eQTL data in dogs or some other laurasiatheria genome? If possible something in a format that can be uploaded or displayed somehow in one of the common genome browsers, like UCSC or Ensembl. ...
genome eqtl written 7.1 years ago by Ahdf-Lell-Kocks1.6k
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Common Viral Dna In Human Sequencing Samples?
... What are the most common viral DNA sequences found in human or other mammalian resequencing samples? I have seen there is an NCBI refseq viral genomes link, but what I would like to know is the common viruses found in normal next generation sequencing experiments. http://biostar.stackexchange.com/q ...
next-gen sequencing written 7.1 years ago by Ahdf-Lell-Kocks1.6k • updated 7.1 years ago by lh331k

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