Sam’s Notebook

University of Washington - Fishery Sciences - Roberts Lab

Posts

Data Wrangling - Panopea generosa Genome Feature Sequence Lengths

  • 1 min read

In preparation for a paper we’re writing, we needed some summary stats on the various genome assembly feature sequences. I determined the max/min, mean, and median sequence lengths for all the GFF feature files we currently have for Pgenerosa_v070, Pgenerosa_v070_top18_scaffolds, and Pgenerosa_v074. This info will be compiled in to a table for the manuscript. See our Genomic Resources wiki for more info on GFFs:

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Genome Comparison - Pgenerosa_v074 vs Pgenerosa_v070 with MUMmer Promer on Mox

  • 3 min read

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that I’ve decided to perform a series of genome comparisons and see how they match up, with an emphasis on Scaffold 1, using MUMmer 3.23 (specifically, promer for protein level comparisons). This software is specifically designed to do this type of comparison.

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Genome Comparison - Pgenerosa_v074 vs S.glomerata NCBI with MUMmer Promer on Mox

  • 3 min read

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that I’ve decided to perform a series of genome comparisons and see how they match up, with an emphasis on Scaffold 1, using MUMmer 3.23 (specifically, promer for protein level comparisons). This software is specifically designed to do this type of comparison.

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Genome Comparison - Pgenerosa_v074 vs M.yessoensis NCBI with MUMmer Promer on Mox

  • 3 min read

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that I’ve decided to perform a series of genome comparisons and see how they match up, with an emphasis on Scaffold 1, using MUMmer 3.23 (specifically, promer for protein level comparisons). This software is specifically designed to do this type of comparison.

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Genome Comparison - Pgenerosa_v074 vs H.sapiens NCBI with MUMmer Promer on Mox

  • 3 min read

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that I’ve decided to perform a series of genome comparisons and see how they match up, with an emphasis on Scaffold 1, using MUMmer 3.23 (specifically, promer for protein level comparisons). This software is specifically designed to do this type of comparison.

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Genome Comparison - Pgenerosa_v074 vs C.virginica NCBI with MUMmer Promer on Mox

  • 3 min read

In continuing to further improve our geoduck genome annotation, I’m attempting to figure out why Scaffold 1 of our assembly doesn’t have any annotations. As part of that I’ve decided to perform a series of genome comparisons and see how they match up, with an emphasis on Scaffold 1, using MUMmer 3.23 (specifically, promer for protein level comparisons). This software is specifically designed to do this type of comparison.

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