/gannet/Atumefaciens/20190710_Pgenerosa_v074_gensas_annotation Annotation of the Panopea generosa genome assembly, via GenSAS: Pgenerosa_v074. --- FILES - Panopea-generosa-vv0.74.a3.5d2cb6212242c-blast_transcript.blast.gff3: Intermediate BLASTn GFF. - Panopea-generosa-vv0.74.a3.5d2cb6366ebcf-blast_protein.blast.gff3: Intermediate BLASTx against Trinity transcriptome(s) GFF. - Panopea-generosa-vv0.74.a3.5d3f05ff5e0bd-augustus.cDNA.fna: Nucleotide FastA of Augustus-predicted cDNA (e.g. mRNA). - Panopea-generosa-vv0.74.a3.5d3f05ff5e0bd-augustus.CDS.fna: Nucleotide FastA of Augustus-predicted coding sequences (CDS). - Panopea-generosa-vv0.74.a3.5d3f05ff5e0bd-augustus.genes.fna: Nucleotide FastA of Augustus-predicted genes. - Panopea-generosa-vv0.74.a3.5d3f05ff5e0bd-augustus.genes.gff3: GFF of Augustus-predicted genes. - Panopea-generosa-vv0.74.a3.5d3f05ff5e0bd-augustus.protein.faa: Amino acid FastA of Augustus-predicted proteins. - Panopea-generosa-vv0.74.a3.5d63f6bf67157-evm.cDNA.fna: Nucleotide FastA of Evidence Modeler-predicted cDNA (e.g. mRNA). - Panopea-generosa-vv0.74.a3.5d63f6bf67157-evm.CDS.fna: Nucleotide FastA of Evidence Modeler-predicted coding sequences (CDS). - Panopea-generosa-vv0.74.a3.5d63f6bf67157-evm.genes.fna: Nucleotide FastA of Evidence Modeler-predicted genes. - Panopea-generosa-vv0.74.a3.5d63f6bf67157-evm.genes.gff3: GFF of Evidence Modeler-predicted genes. - Panopea-generosa-vv0.74.a3.5d63f6bf67157-evm.protein.faa: Amino acid FastA of Evidence Modeler-predicted proteins. - Panopea-generosa-vv0.74.a3.5d652f676e026-pasa_refine.cDNA.fna: Nucleotide FastA of PASA-refinement of predicted cDNA (e.g. mRNA). - Panopea-generosa-vv0.74.a3.5d652f676e026-pasa_refine.CDS.fna: Nucleotide FastA of PASA-refinement of predicted coding sequences (CDS). - Panopea-generosa-vv0.74.a3.5d652f676e026-pasa_refine.genes.fna: Nucleotide FastA of PASA-refinement of predicted genes. - Panopea-generosa-vv0.74.a3.5d652f676e026-pasa_refine.genes.gff3: GFF of PASA-refinement of predicted genes. - Panopea-generosa-vv0.74.a3.5d652f676e026-pasa_refine.protein.faa: Amino acid FastA of PASA-refinement of predicted protens. - Panopea-generosa-vv0.74.a3.5d65aa9aa46a4-blast_functional.tab: BLASTp output of GenSAS-predicted genes against P.generosa Transdecoder peptides. - Panopea-generosa-vv0.74.a3.5d65aa9fceb75-diamond_functional.tab: DIAMOND output of GenSAS-predicted genes against P.generosa Transdecoder peptides. - Panopea-generosa-vv0.74.a3.5d65aaa22961e-interproscan.tab: InterProScan output of GenSAS-predicted genes. Includes gene ontology (GO) terms. - Panopea-generosa-vv0.74.a3.5d65aaa449919-pfam.tab: Pfam output of GenSAS-predicted genes. - Panopea-generosa-vv0.74.a3.5d65aaa7d4810-signalp.tab: SignalP output of GenSAS-predicted genes. - Panopea-generosa-vv0.74.a3.5d66e4d277096-diamond_protein.diamond.gff3: GFF of DIAMOND output with SwissProt accessions. - Panopea-generosa-vv0.74.a3.5d66e50df21de-getorf.orfs.gff3: GFF of predicted open reading frames (ORF), generated by EMBOSS getorf. - Panopea-generosa-vv0.74.a3.5d66e5e537f02-blast_functional.tab: BLASTp output of GenSAS-predicted mRNAs against SwissProt. - Panopea-generosa-vv0.74.a3.5d66e5f03c48d-diamond_functional.tab: DIAMOND output of GenSAS-predicted mRNAs against SwissProt. - Panopea-generosa-vv0.74.a3.5d6843e21278a-publish.cDNA.fna: Nucleotide FastA of finalized GenSAS-predicted cDNA (e.g. mRNA). - Panopea-generosa-vv0.74.a3.5d6843e21278a-publish.CDS.fna: Nucleotide FastA of finalized GenSAS-predicted coding sequences (CDS). - Panopea-generosa-vv0.74.a3.5d6843e21278a-publish.genes.fna: Nucleotide FastA of finalized GenSAS-predicted genes. - Panopea-generosa-vv0.74.a3.5d6843e21278a-publish.genes.gff3: GFF of finalized GenSAS annotation. Seems to be virtually the same as Panopea-generosa-vv0.74.a3-merged-2019-09-03-6-14-33.gff3. - Panopea-generosa-vv0.74.a3.5d6843e21278a-publish.protein.faa: Amino acid FastA of finalized GenSAS-predicted proteins. - Panopea-generosa-vv0.74.a3.CDS.gff3: GFF of just coding sequences (CDS) from Panopea-generosa-vv0.74.a3-merged-2019-09-03-6-14-33.gff3. - Panopea-generosa-vv0.74.a3.exon.gff3: GFF of just exons from Panopea-generosa-vv0.74.a3-merged-2019-09-03-6-14-33.gff3. - Panopea-generosa-vv0.74.a3.gene.gff3: GFF of just genes from Panopea-generosa-vv0.74.a3-merged-2019-09-03-6-14-33.gff3. - Panopea-generosa-vv0.74.a3-merged-2019-09-24-9-20-04.gff3: GFF of all features "merged." Has SwissProt IDs, and algorithm used to match to SP ID (e.g. BLASTp or DIAMOND) in Column 9. Seems to be virtually the same as Panopea-generosa-vv0.74.a3.5d6843e21278a-publish.genes.gff3. - Panopea-generosa-vv0.74.a3.mRNA.gff3: GFF of just mRNA from Panopea-generosa-vv0.74.a3-merged-2019-09-03-6-14-33.gff3. - t_5d25021b0d20b-5d250896def4c-repeatmasker.gensas.gff3: GFF of RepeatMasker repeat/transposable elements. - t_5d25021b0d20b-5d6843e21278a-publish-project-summary.txt: Text file summarizing all the GenSAS jobs that were run, along with their respective settings. --- Notebook: https://robertslab.github.io/sams-notebook/2019/07/10/Genome-Annotation-Pgenerosa_v074-Using-GenSAS.html