Posts
Data Wrangling - Pgenerosa_v074.a3 Annotation Genome Repeats Compostion
Needed to pull some numbers on repeats in our Pgenerosa_v074.a3 GenSAS annotation (from 20190710) for the manuscript we’re putting together.
Data Wrangling - Pgenerosa_v074.a3 Annotation Genome Feature Sequence Lengths
The GenSAS Pgenerosa_v074 annotation from 20190710 (referred to as: Panopea-generosa-vv0.74.a3) recently completed (after nearly a month of running).
Data Wrangling - Panopea generosa Genome Feature Sequence Lengths
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:
Data Wrangling - Create a CpG GFF from Pgenerosa_v074 using EMBOSS fuzznuc on Swoose
Steven wanted me to create a CpG GFF for use in IGV visulations for continued Pgenerosa_v074 analysis. I did that by running the EMBOSS tool fuzznuc:
Genome Annotation - Pgenerosa_v074 MAKER on Mox with Stringtie Transcripts GFF
For reference, this annotation will be referred to as Pgenerosa_v074.1.
Genome Comparison - Pgenerosa_v074 vs Pgenerosa_v070 with MUMmer Promer on Mox
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.
Genome Comparison - Pgenerosa_v074 vs S.glomerata NCBI with MUMmer Promer on Mox
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.
Genome Comparison - Pgenerosa_v074 vs M.yessoensis NCBI with MUMmer Promer on Mox
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.
Genome Comparison - Pgenerosa_v074 vs H.sapiens NCBI with MUMmer Promer on Mox
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.
Genome Comparison - Pgenerosa_v074 vs C.virginica NCBI with MUMmer Promer on Mox
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.