Sam’s Notebook

University of Washington - Fishery Sciences - Roberts Lab

Posts - Page 2 of 109

Genome Comparison - Pgenerosa_v074 vs M.yessoensis NCBI with MUMmer 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 (v4) (specifically, nucmer for nucleotide 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 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 (v4) (specifically, nucmer for nucleotide comparisons). This software is specifically designed to do this type of comparison.

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Genome Comparison - Pgenerosa_v074 vs C.gigas NCBI with MUMmer 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 (v4) (specifically, nucmer for nucleotide 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 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 (v4) (specifically, nucmer for nucleotide comparisons). This software is specifically designed to do this type of comparison.

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Data Summary - P.generosa Transcriptome Assemblies Stats

  • 1 min read

In our continuing quest to wrangle the geoduck transcriptome assemblies we have, I was tasked with compiling assembly stats for our various assemblies. The table below provides an overview of some stats for each of our assemblies. Links within the table go to the the notebook entries for the various methods from which the data was gathered. In general:

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Genome Annotation - Pgenerosa_v074 Transcript Isoform ID with Stringtie on Mox

  • 4 min read

After annotating Pgenerosa_v070 and comparing feature counts, there was a drastic difference between the two genome versions. Additionally, both of those genomes ended up with no CDS/exon/gene/mRNA features identified in the largest scaffold. So, to explore this further by seeing where (if??) sequencing reads map to the scaffold, and to obtain transcript isoforms for the genome, I ran Stringtie. A Hisat2 index was prepared earlier.

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Genome Annotation - Pgenerosa_v070 Transcript Isoform ID with Stringtie on Mox

  • 3 min read

After annotating Pgenerosa_v074 and comparing feature counts, there was a drastic difference between the two genome versions. Additionally, both of those genomes ended up with no CDS/exon/gene/mRNA features identified in the largest scaffold. So, to explore this further by seeing where (if??) sequencing reads map to the scaffold, and to obtain transcript isoforms for the genome, I ran Stringtie. A Hisat2 index was prepared earlier.

Read More