Posts
Genome Assessment - BUSCO Metazoa on Pgenerosa_v074 on Mox
Ran BUSCO on Mox for our Pgenerosa_v74 genome assembly to assess “completeness”. This is the assembly that only has the longest 18 scaffolds (the scaffolds hand-curated by Phase Genomics).
Genome Assessment - BUSCO Metazoa on Pgenerosa_v70 on Mox
Ran BUSCO on Mox for our Pgenerosa_v70 genome assembly to assess “completeness”.
Genome Annotation - Pgenerosa_v074 MAKER on Mox
I previously created a subset of the Pgenerosa_v070 genome assembly that contains just the largest 18 scaffolds (these scaffolds were produced by Phase Genomics, utilizing some Hi-C sequencing). The new subsetted genome is labeled as Pgenerosa_v074.fa (914MB).
Transcriptome Annotation - Geoduck Larvae Day5 EPI99 with Transdecoder on Mox
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Transcriptome Annotation - Geoduck Super Low OA EPI116 with Transdecoder on Mox
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Transcriptome Annotation - Geoduck Juvenile Super Low OA EPI115 with Transdecoder on Mox
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Transcriptome Annotation - Geoduck Juvenile Ambient OA EPI124 with Transdecoder on Mox
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Transcriptome Annotation - Geoduck Juvenile Ambient OA EPI123 with Transdecoder on Mox
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Transcriptome Annotation - Geoduck Gonad with Transdecoder on Mox
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.
Transcriptome Annotation - Geoduck Ctenidia with Transdecoder on Mox
Used Transdecoder to identify open reading frames (ORFs) for use in annotating Pgenerosa_v074 genome assembly. Relies on BLASTp, Pfam, and HMM scanning to ID ORFs.