Shelly posted a GitHub Issue asking if I could create a file of S.salar genes with their UniProt annotations (e.g. gene name, UniProt accession, GO terms).

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After attempting to submit our Ostrea lurida (Olympia oyster) genome assembly annotations (via GFF) to NCBI, the submission process also highlighted some short comings of the Olurida_v081 assembly. When getting ready to submit the genome annotations to NCBI, I was required to calculate the genome coverage we had. NCBI suggested to calculate this simply by counting the number of bases sequenced and divide it by the genome size. Doing this resulted in an estimated coverage of ~55X coverage, yet we have significant stretches of Ns throughout the assembly. I understand why this is still technically possible, but it’s just sticking in my craw. So, I’ve decided to set up a quick assembly to see what I can come up with. Of note, the canonical assembly we’ve been using relied on the scaffolded assembly provided by BGI; we never attempted our own assembly from the raw data.

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Per this GitHub Issue, Steven has asked to get our Ostrea lurida (Olympia oyster) genome assembly (Olurida_v081.fa) submitted to NCBI with annotations. The first step in the submission process is to use the NCBI table2asn_GFF software to validate the FastA assembly, as well as the GFF annotations file. Once the software has been run, it will point out any errors which need to be corrected prior to submission.

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Decided to tackle this GitHub Issue about creating a transposable elements IGV track with the new Roslin C.gigas genome, since it had been sitting for a while and I have code sitting around that’s ready to roll for this type of thing.

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Aidan recently needed to use R on a machine with more memory. Additionally, it would be ideal if he could use RStudio. So, I managed to figure out how to set up a Singularity container running rocker/rstudio.

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To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect of the pipeline manually, as I continue to have issues utilizing the automatic pipeline. As such, I’ve run minimap2 according to the BlobToolKit “Getting Started” guide on Mox. This will map the trimmed 10x-Genomics reads from 20210401 to the Panopea-generosa-v1.0.fa assembly (FastA; 914MB).

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To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect of the pipeline manually, as I continue to have issues utilizing the automatic pipeline. As such, I’ve run DIAMOND BLASTx according to the BlobToolKit “Getting Started” guide on Mox.

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To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect of the pipeline manually, as I continue to have issues utilizing the automatic pipeline. As such, I’ve run BLASTn according to the BlobToolKit “Getting Started” guide on Mox.

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Steven asked me to try running Blob Tool Kit to identify potential contaminating sequence in our Panopea generosa (Pacific geoduck) genome assembly (v1.0). In preparation for running Blob Tool Kit, I needed to trim the 10x Genomics FastQ data used by Phase Genomics. Files were trimmed using fastp on Mox.

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Continued annotation of cbai_transcriptome_v4.0.fasta [Trinity de novo assembly from 20210317(https://robertslab.github.io/sams-notebook/2021/03/17/Transcriptome-Assembly-C.bairdi-Transcriptome-v4.0-Using-Trinity-on-Mox.html)] using Trinotate on Mox. This will provide a thorough annotation, including genoe ontology (GO) term assignments to each contig.

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