DOI: 10.5061/dryad.jn8t1
title: Data from: "Transcriptomic resources for five shrimp (Crustacea: Atyidae and Alpheidae) species from the anchialine ecosystem" in Genomic Resources Notes accepted 1 June 2014 to 31 July 2014

description: [No abstract entered]
description: Antecaridina_lauensis_transcriptomeFile containing contigs in FASTA format from Antecaridina lauensis assembled de novo using Trinity.Antecaridina_lauensis_TRI_1_20_2014_NORM.fastaAntecaridina_lauensis_bedAntecaridina lauensis .bed file containing information for putative ORFs as called by the program TransDecoderAntecaridina_lauensis_TRI_1_20_2014_NORM.fasta.transdecoder.bedAntecaridina_lauensis_cdsAntecaridina lauensis .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoderAntecaridina_lauensis_TRI_1_20_2014_NORM.fasta.transdecoder.cdsAntecaridina_lauensis_gffAntecaridina lauensis .gff file containing mapping information for the putative ORFs as called by the program TransDecoderAntecaridina_lauensis_TRI_1_20_2014_NORM.fasta.transdecoder.gff3Antecaridina_lauensis_pepAntecaridina lauensis .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoderAntecaridina_lauensis_TRI_1_20_2014_NORM.fasta.transdecoder.pepAntecaridina_lauensis_Trinotate_Annotation_ReportAntecaridina lauensis transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program TrinotateCaridina_rubella_transcriptomeFile containing contigs in FASTA format from Caridina rubella assembled de novo using Trinity.Caridina_rubella_TRI_1_20_2014_NORM.fastaCaridina_rubella_bedCaridina rubella .bed file containing information for putative ORFs as called by the program TransDecoderCaridina_rubella_TRI_1_20_2014_NORM.fasta.transdecoder.bedCaridina_rubella_cdsCaridina rubella .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoderCaridina_rubella_TRI_1_20_2014_NORM.fasta.transdecoder.cdsCaridina_rubella_gffCaridina rubella .gff file containing mapping information for the putative ORFs as called by the program TransDecoderCaridina_rubella_TRI_1_20_2014_NORM.fasta.transdecoder.gff3Caridina_rubella_pepCaridina rubella .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoderCaridina_rubella_TRI_1_20_2014_NORM.fasta.transdecoder.pepCaridina_rubella_Trinotate_Annotation_ReportCaridina rubella transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program TrinotateHalocaridinides_trigonopthalma_transcriptomeFile containing contigs in FASTA format from Halocaridinides trigonophthalma assembled de novo using Trinity.Halocaridinides_trigonopthalma_TRI_1_20_2014_NORM.fastaHalocaridinides_trigonopthalma_bedHalocaridinides trigonophthalma .bed file containing information for putative ORFs as called by the program TransDecoderHalocaridinides_trigonopthalma_TRI_1_20_2014_NORM.fasta.transdecoder.bedHalocaridinides_trigonopthalma_cdsHalocaridinides trigonophthalma .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoderHalocaridinides_trigonopthalma_TRI_1_20_2014_NORM.fasta.transdecoder.cdsHalocaridinides_trigonopthalma_gffHalocaridinides trigonophthalma .gff file containing mapping information for the putative ORFs as called by the program TransDecoderHalocaridinides_trigonopthalma_TRI_1_20_2014_NORM.fasta.transdecoder.gff3Halocaridinides_trigonopthalma_pepHalocaridinides trigonophthalma .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoderHalocaridinides_trigonopthalma_TRI_1_20_2014_NORM.fasta.transdecoder.pepHalocaridinides_trigonopthalma_Trinotate_Annotation_ReportHalocaridinides trigonophthalma transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program TrinotateMetabetaeus_lohena_transcriptomeFile containing contigs in FASTA format from Metabetaeus lohena assembled de novo using Trinity.Metabetaeus_lohena_TRI_1_17_2014_NORM.fastaMetabetaeus_lohena_bedMetabetaeus lohena .bed file containing information for putative ORFs as called by the program TransDecoderMetabetaeus_lohena_TRI_1_17_2014_NORM.fasta.transdecoder.bedMetabetaeus_lohena_cdsMetabetaeus lohena .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoderMetabetaeus_lohena_TRI_1_17_2014_NORM.fasta.transdecoder.cdsMetabetaeus_lohena_gffMetabetaeus lohena .gff file containing mapping information for the putative ORFs as called by the program TransDecoderMetabetaeus_lohena_TRI_1_17_2014_NORM.fasta.transdecoder.gff3Metabetaeus_lohena_pepMetabetaeus lohena .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoderMetabetaeus_lohena_TRI_1_17_2014_NORM.fasta.transdecoder.pepMetabetaeus_lohena_Trinotate_Annotation_ReportMetabetaeus lohena transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program TrinotateMetabetaeus_minutus_transcriptomeFile containing contigs in FASTA format from Metabetaeus minutus assembled de novo using Trinity.Metabetaeus_minutus_TRI_1_20_2014_NORM.fastaMetabetaeus_minutus_bedMetabetaeus minutus .bed file containing information for putative ORFs as called by the program TransDecoderMetabetaeus_minutus_TRI_1_20_2014_NORM.fasta.transdecoder.bedMetabetaeus_minutus_cdsMetabetaeus minutus .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoderMetabetaeus_minutus_TRI_1_20_2014_NORM.fasta.transdecoder.cdsMetabetaeus_minutus_gffMetabetaeus minutus .gff file containing mapping information for the putative ORFs as called by the program TransDecoderMetabetaeus_minutus_TRI_1_20_2014_NORM.fasta.transdecoder.gff3Metabetaeus_minutus_pepMetabetaeus minutus .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoderMetabetaeus_minutus_TRI_1_20_2014_NORM.fasta.transdecoder.pepMetabetaeus_minutus_Trinotate_Annotation_ReportMetabetaeus minutus transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program TrinotateAll_orthologous_clustersA compressed file containing 25,742 files that describe 12,871 orthologous clusters. Each cluster has two files associated with it: one of unaligned sequences in FASTA format (ending in .fasta) and one with sequences that were aligned using ClustalO (ending in .fasta_clustalo). Orthologous clusters were generated using ORthoMCL and the putative ORFs from each of the five anchialine shrimp transcriptomes.Filtered_subset_orthologous_clustersA compressed file consisting of 1,784 files describing the 892 orthologous clusters that contained a single ortholog from each of the five anchialine shrimp species. For each orthologous cluster there are two files: one file contains unaligned sequence files in fasta format (ending in .fasta) and one file contains sequences that were aligned using ClustalO (ending in .fasta_clustalo). Orthologous clusters were identified using OrthoMCL and the putative ORFs from the five anchialine shrimp species.cd_hit_dataA compressed file consisting of 10 cd hit files (2 for each of the 5 anchialine shrimp species) files used to generate orthologous clusters from the five anchialine shrimp species. One file (ending in .cd-hit_filtered) contains the putative ORFs used to generate clusters while the other file (ending in .cd-hit_filtered.clstr) contains statistics and information on the clusters.compliant_Fasta_filesA compressed file consisting of 5 files (1 from each of the five anchialine shrimp species) with the putative ORF amino acid sequences from each species used to generate orthologous clusters.compliantFasta.zipRemapping_expressionA compressed file consisting of five Excel spreadsheets (one for each anchialine shrimp species) describing the remapping of raw reads onto the assembled contigs in order to infer expression. There are two spreadsheets per file: the first (name ending in _counts) gives the number of remapped reads (in the Counts column), the length (in the Length column), and the FPKM values (in the FPKM column) for each contig/Trinity subcomponent. The second spreadsheet (name ending in _highExpress) has annotation details for the top 0.1% of highly expressed contigs/Trinity subcomponents.Assembly_scriptThis bash script will concatenated, digitally normalize, and assemble (via Trinity) paired end .fastq files. See comments for usage, and if script is modified, please provide proper attribution.copy_concat_norm_TRI_hudAlpha_HISEQ2500.shTrinotateThis script will generate a Trinotate annotation compressed file for a .fasta Trinity assembly. See comments for usage, and if script is modified, please provide proper attribution.auto_Trinotate.shgenerate_Trinotate_reportThis script will generate a tab-delimited report from a Trinotate annotation compressed file. See comments for usage, and if script is modified, please provide proper attribution.fasta_statsThis script will generate summary statistics from an assembled Trinity fasta file. See comments for usage, and if script is modified, please provide proper attribution.Ortho1This is the first script (of 2) that will generate the OrthoMCL files discussed in the manuscript. See comments for usage, and if script is modified, please provide proper attribution.Ortho2This is the second script (of 2) that will generate the OrthoMCL files described in the manuscript. See comments for usage, and if script is modified, please provide proper attribution.clustalAlignThis script will align fasta file (e.g., those generated by OrthoMCL) using ClustalO. See comments for usage, and if script is modified, please provide proper attribution.MappingThis script will map .fastq reads to a .fasta assembly file and generate a tab-delimited table of counts of reads that mapped back to each Trinity subcomponent. See comments for usage, and if script is modified, please provide proper attribution.