/gannet/Atumefaciens/20190928_Pgenerosa_v074.a4_gensas_annotation Further annotation of the Panopea generosa genome assembly, via GenSAS: Pgenerosa_v074. The majority of files in this directory are GenSAS "intermediate" files. Refer to the notebook (URL at end of this document) for links to the most useful/relevant files to use for analysis. --- FILES - Panopea-generosa-vv0.74.a4.5d250896def4c-repeatmasker.repeats.fna: Nucleotide FastA of RepeatMasker repeats. - Panopea-generosa-vv0.74.a4.5d250896def4c-repeatmasker.repeats.gff3: GFF of RepeatMasker repeats. - Panopea-generosa-vv0.74.a4.5d25089d78791-repeatmodeler.repeats.fna: Nucleotide FastA of RepeatModeler repeats. - Panopea-generosa-vv0.74.a4.5d25089d78791-repeatmodeler.repeats.gff3: GFF of RepeatModeler repeats. - Panopea-generosa-vv0.74.a4.5d2cb6212242c-blast_transcript.blast.gff3: Intermediate BLASTn GFF. - Panopea-generosa-vv0.74.a4.5d2cb6366ebcf-blast_protein.blast.gff3: Intermediate BLASTx against Trinity transcriptome(s) GFF. - Panopea-generosa-vv0.74.a4.5d3f05ff5e0bd-augustus.cDNA.fna: (Augustus-02) Nucleotide FastA of Augustus-predicted cDNA (e.g. mRNA). - Panopea-generosa-vv0.74.a4.5d3f05ff5e0bd-augustus.CDS.fna: (Augustus-02) Nucleotide FastA of Augustus-predicted coding sequences (CDS). - Panopea-generosa-vv0.74.a4.5d3f05ff5e0bd-augustus.genes.fna: (Augustus-02) Nucleotide FastA of Augustus-predicted genes. - Panopea-generosa-vv0.74.a4.5d3f05ff5e0bd-augustus.genes.gff3: (Augustus-02) GFF of Augustus-predicted genes. - Panopea-generosa-vv0.74.a4.5d3f05ff5e0bd-augustus.protein.faa: (Augustus-02) Amino acid FastA of Augustus-predicted proteins. - Panopea-generosa-vv0.74.a4.5d3f060cddf32-snap.cDNA.fna: Nucleotide FastA of SNAP-predicted cDNA (e.g. mRNA). - Panopea-generosa-vv0.74.a4.5d3f060cddf32-snap.CDS.fna: Nucleotide FastA of SNAP-predicted coding sequences (CDS). - Panopea-generosa-vv0.74.a4.5d3f060cddf32-snap.genes.fna: Nucleotide FastA of SNAP-predicted genes. - Panopea-generosa-vv0.74.a4.5d3f060cddf32-snap.genes.gff3: GFF of SNAP-predicted genes. - Panopea-generosa-vv0.74.a4.5d3f060cddf32-snap.protein.faa: Amino acid FastA of SNAP-predicted proteins. - Panopea-generosa-vv0.74.a4.5d66e4d277096-diamond_protein.diamond.gff3: GFF of DIAMOND output with SwissProt accessions. - Panopea-generosa-vv0.74.a4.5d66e50df21de-getorf.orfs.gff3: GFF of predicted open reading frames (ORF), generated by EMBOSS getorf. - Panopea-generosa-vv0.74.a4.5d82b23f69545-braker.cDNA.fna: Nucleotide FastA of BRAKER-predicted cDNA (e.g. mRNA). - Panopea-generosa-vv0.74.a4.5d82b23f69545-braker.CDS.fna: Nucleotide FastA of BRAKER-predicted coding sequences (CDS). - Panopea-generosa-vv0.74.a4.5d82b23f69545-braker.genes.fna: Nucleotide FastA of BRAKER-predicted genes. - Panopea-generosa-vv0.74.a4.5d82b23f69545-braker.genes.gff3: GFF of BRAKER-predicted genes. - Panopea-generosa-vv0.74.a4.5d82b23f69545-braker.protein.faa: Amino acid FastA of BRAKER-predicted proteins. - Panopea-generosa-vv0.74.a4.5d82b2b6570c8-augustus.cDNA.fna: (Augustus-01) Nucleotide FastA of Augustus-predicted cDNA (e.g. mRNA). - Panopea-generosa-vv0.74.a4.5d82b2b6570c8-augustus.CDS.fna: (Augustus-01) Nucleotide FastA of Augustus-predicted coding sequences (CDS). - Panopea-generosa-vv0.74.a4.5d82b2b6570c8-augustus.genes.fna: (Augustus-01) Nucleotide FastA of Augustus-predicted genes. - Panopea-generosa-vv0.74.a4.5d82b2b6570c8-augustus.genes.gff3: (Augustus-01) GFF of Augustus-predicted genes. - Panopea-generosa-vv0.74.a4.5d82b2b6570c8-augustus.protein.faa: (Augustus-01) Amino acid FastA of Augustus-predicted proteins. - Panopea-generosa-vv0.74.a4.5d82b2fdbf06f-genemark.cDNA.fna: Nucleotide FastA of GeneMarkES-predicted cDNA (e.g. mRNA). - Panopea-generosa-vv0.74.a4.5d82b2fdbf06f-genemark.CDS.fna: Nucleotide FastA of GeneMarkES-predicted coding sequences (CDS). - Panopea-generosa-vv0.74.a4.5d82b2fdbf06f-genemark.genes.fna: Nucleotide FastA of GeneMarkES-predicted genes. - Panopea-generosa-vv0.74.a4.5d82b2fdbf06f-genemark.genes.gff3: GFF of GeneMarkES-predicted genes. - Panopea-generosa-vv0.74.a4.5d82b2fdbf06f-genemark.protein.faa: Amino acid FastA of GeneMarkES-predicted proteins. - Panopea-generosa-vv0.74.a4.5d82b316cd298-trnascan.tRNA.fna: Nucleotide FastA of tRNAscan predictions. - Panopea-generosa-vv0.74.a4.5d82b316cd298-trnascan.tRNA.gff3: GFF of tRNAscan predictions. - Panopea-generosa-vv0.74.a4.5d82b32022812-rnammer.rRNA.fna: Nucleotide FastA of RNAmmer predictions. - Panopea-generosa-vv0.74.a4.5d82b32022812-rnammer.rRNA.gff3: GFF of RNAmmer predictions. - Panopea-generosa-vv0.74.a4.5d8fcb23b2ad2-evm.cDNA.fna: Nucleotide FastA of Evidence Modeler-predicted cDNA (e.g. mRNA). - Panopea-generosa-vv0.74.a4.5d8fcb23b2ad2-evm.CDS.fna: Nucleotide FastA of Evidence Modeler-predicted coding sequences (CDS). - Panopea-generosa-vv0.74.a4.5d8fcb23b2ad2-evm.genes.fna: Nucleotide FastA of Evidence Modeler-predicted genes. - Panopea-generosa-vv0.74.a4.5d8fcb23b2ad2-evm.genes.gff3: GFF of Evidence Modeler-predicted genes. - Panopea-generosa-vv0.74.a4.5d8fcb23b2ad2-evm.protein.faa: Amino acid FastA of Evidence Modeler-predicted proteins. - Panopea-generosa-vv0.74.a4.5d938f378020d-pasa_refine.cDNA.fna: Nucleotide FastA of PASA-refinement of predicted cDNA (e.g. mRNA). - Panopea-generosa-vv0.74.a4.5d938f378020d-pasa_refine.CDS.fna: Nucleotide FastA of PASA-refinement of predicted coding sequences (CDS). - Panopea-generosa-vv0.74.a4.5d938f378020d-pasa_refine.genes.fna: Nucleotide FastA of PASA-refinement of predicted genes. - Panopea-generosa-vv0.74.a4.5d938f378020d-pasa_refine.genes.gff3: GFF of PASA-refinement of predicted genes. - Panopea-generosa-vv0.74.a4.5d938f378020d-pasa_refine.protein.faa: Amino acid FastA of PASA-refinement of predicted protens. - Panopea-generosa-vv0.74.a4.5d951a9b74287-blast_functional.tab: BLASTp output of GenSAS-predicted mRNAs against SwissProt. - Panopea-generosa-vv0.74.a4.5d951bcf45b4b-diamond_functional.tab: DIAMOND output of GenSAS-predicted mRNAs against SwissProt. - Panopea-generosa-vv0.74.a4.5d951bd337e9d-interproscan.tab: InterProScan output of GenSAS-predicted genes. Includes gene ontology (GO) terms. - Panopea-generosa-vv0.74.a4.5d951bd7b0381-pfam.tab: Pfam output of GenSAS-predicted genes. - Panopea-generosa-vv0.74.a4.5d951be7708d2-signalp.tab: SignalP output of GenSAS-predicted genes. - Panopea-generosa-vv0.74.a4.5d9637f372b5d-publish.cDNA.fna: Nucleotide FastA of finalized GenSAS-predicted cDNA (e.g. mRNA). - Panopea-generosa-vv0.74.a4.5d9637f372b5d-publish.CDS.fna: Nucleotide FastA of finalized GenSAS-predicted coding sequences (CDS). - Panopea-generosa-vv0.74.a4.5d9637f372b5d-publish.genes.fna: Nucleotide FastA of finalized GenSAS-predicted genes. - Panopea-generosa-vv0.74.a4.5d9637f372b5d-publish.genes.gff3: GFF of finalized GenSAS annotation. Seems to be virtually the same as Panopea-generosa-vv0.74.a4-merged-2019-10-07-4-46-46.gff3. - Panopea-generosa-vv0.74.a4.5d9637f372b5d-publish.protein.faa: Amino acid FastA of finalized GenSAS-predicted proteins. - Panopea-generosa-vv0.74.a4-BUSCO.summary.txt: BUSCO summary of annotated genome. - Panopea-generosa-vv0.74.a4.CDS.gff3: GFF of just coding sequences (CDS) from Panopea-generosa-vv0.74.a4-merged-2019-10-07-4-46-46.gff3 - Panopea-generosa-vv0.74.a4.exon.gff3: GFF of just exons from Panopea-generosa-vv0.74.a4-merged-2019-10-07-4-46-46.gff3 - Panopea-generosa-vv0.74.a4.gene.gff3: GFF of just genes from Panopea-generosa-vv0.74.a4-merged-2019-10-07-4-46-46.gff3 - Panopea-generosa-vv0.74.a4-merged-2019-10-07-4-46-46.gff3: GFF of all features "mergePanopea-generosa-vv0.74.a4.5d9637f372b5d-publish.genes.gff3. - Panopea-generosa-vv0.74.a4.mRNA.gff3: GFF of just mRNA from Panopea-generosa-vv0.74.a4-merged-2019-10-07-4-46-46.gff3 - Panopea-generosa-vv0.74.a4.repeat_region.gff3: GFF of just repeat regions from Panopea-generosa-vv0.74.a4-merged-2019-10-07-4-46-46.gff3 - Panopea-generosa-vv0.74.a4.rRNA.gff3: GFF of rRNA from Panopea-generosa-vv0.74.a4-merged-2019-10-07-4-46-46.gff3 - Panopea-generosa-vv0.74.a4.tRNA.gff3: GFF of tRNA from Panopea-generosa-vv0.74.a4-merged-2019-10-07-4-46-46.gff3 - t_5d25021b0d20b-5d9637f372b5d-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/2019/09/28/Genome-Annotation-Pgenerosa_v074-a4-Using-GenSAS.html