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

Havird JC, Santos SR

Date Published: October 27, 2014

DOI: http://dx.doi.org/10.5061/dryad.jn8t1

 

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Title Antecaridina_lauensis_transcriptome
Downloaded 29 times
Description File containing contigs in FASTA format from Antecaridina lauensis assembled de novo using Trinity.
Download Antecaridina_lauensis_TRI_1_20_2014_NORM.fasta (112.2 Mb)
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Title Antecaridina_lauensis_bed
Downloaded 12 times
Description Antecaridina lauensis .bed file containing information for putative ORFs as called by the program TransDecoder
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Title Antecaridina_lauensis_cds
Downloaded 8 times
Description Antecaridina lauensis .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoder
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Title Antecaridina_lauensis_gff
Downloaded 8 times
Description Antecaridina lauensis .gff file containing mapping information for the putative ORFs as called by the program TransDecoder
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Title Antecaridina_lauensis_pep
Downloaded 10 times
Description Antecaridina lauensis .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoder
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Title Antecaridina_lauensis_Trinotate_Annotation_Report
Downloaded 6 times
Description Antecaridina lauensis transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program Trinotate
Download Antecaridina_lauensis_Trinotate_Annotatio...14.tab (71.82 Mb)
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Title Caridina_rubella_transcriptome
Downloaded 7 times
Description File containing contigs in FASTA format from Caridina rubella assembled de novo using Trinity.
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Title Caridina_rubella_bed
Downloaded 4 times
Description Caridina rubella .bed file containing information for putative ORFs as called by the program TransDecoder
Download Caridina_rubella_TRI_1_20_2014_NORM.fasta...er.bed (2.027 Mb)
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Title Caridina_rubella_cds
Downloaded 5 times
Description Caridina rubella .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoder
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Title Caridina_rubella_gff
Downloaded 2 times
Description Caridina rubella .gff file containing mapping information for the putative ORFs as called by the program TransDecoder
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Title Caridina_rubella_pep
Downloaded 5 times
Description Caridina rubella .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoder
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Title Caridina_rubella_Trinotate_Annotation_Report
Downloaded 9 times
Description Caridina rubella transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program Trinotate
Download Caridina_rubella_Trinotate_Annotation_Rep...14.tab (17.62 Mb)
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Title Halocaridinides_trigonopthalma_transcriptome
Downloaded 10 times
Description File containing contigs in FASTA format from Halocaridinides trigonophthalma assembled de novo using Trinity.
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Title Halocaridinides_trigonopthalma_bed
Downloaded 6 times
Description Halocaridinides trigonophthalma .bed file containing information for putative ORFs as called by the program TransDecoder
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Title Halocaridinides_trigonopthalma_cds
Downloaded 3 times
Description Halocaridinides trigonophthalma .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoder
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Title Halocaridinides_trigonopthalma_gff
Downloaded 4 times
Description Halocaridinides trigonophthalma .gff file containing mapping information for the putative ORFs as called by the program TransDecoder
Download Halocaridinides_trigonopthalma_TRI_1_20_20....gff3 (81.92 Mb)
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Title Halocaridinides_trigonopthalma_pep
Downloaded 4 times
Description Halocaridinides trigonophthalma .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoder
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Title Halocaridinides_trigonopthalma_Trinotate_Annotation_Report
Downloaded 4 times
Description Halocaridinides trigonophthalma transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program Trinotate
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Title Metabetaeus_lohena_transcriptome
Downloaded 8 times
Description File containing contigs in FASTA format from Metabetaeus lohena assembled de novo using Trinity.
Download Metabetaeus_lohena_TRI_1_17_2014_NORM.fasta (143.0 Mb)
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Title Metabetaeus_lohena_bed
Downloaded 5 times
Description Metabetaeus lohena .bed file containing information for putative ORFs as called by the program TransDecoder
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Title Metabetaeus_lohena_cds
Downloaded 5 times
Description Metabetaeus lohena .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoder
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Title Metabetaeus_lohena_gff
Downloaded 4 times
Description Metabetaeus lohena .gff file containing mapping information for the putative ORFs as called by the program TransDecoder
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Title Metabetaeus_lohena_pep
Downloaded 4 times
Description Metabetaeus lohena .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoder
Download Metabetaeus_lohena_TRI_1_17_2014_NORM.fas...er.pep (36.27 Mb)
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Title Metabetaeus_lohena_Trinotate_Annotation_Report
Downloaded 7 times
Description Metabetaeus lohena transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program Trinotate
Download Metabetaeus_lohena_Trinotate_Annotation_R...14.tab (74.97 Mb)
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Title Metabetaeus_minutus_transcriptome
Downloaded 8 times
Description File containing contigs in FASTA format from Metabetaeus minutus assembled de novo using Trinity.
Download Metabetaeus_minutus_TRI_1_20_2014_NORM.fasta (28.08 Mb)
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Title Metabetaeus_minutus_bed
Downloaded 7 times
Description Metabetaeus minutus .bed file containing information for putative ORFs as called by the program TransDecoder
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Title Metabetaeus_minutus_cds
Downloaded 5 times
Description Metabetaeus minutus .cds file containing the nucleotide sequences for coding regions of putative ORFs as called by the program TransDecoder
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Title Metabetaeus_minutus_gff
Downloaded 3 times
Description Metabetaeus minutus .gff file containing mapping information for the putative ORFs as called by the program TransDecoder
Download Metabetaeus_minutus_TRI_1_20_2014_NORM.fas....gff3 (20.12 Mb)
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Title Metabetaeus_minutus_pep
Downloaded 3 times
Description Metabetaeus minutus .pep file containing amino acid sequences for putative ORFs as called by the program TransDecoder
Download Metabetaeus_minutus_TRI_1_20_2014_NORM.fa...er.pep (9.658 Mb)
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Title Metabetaeus_minutus_Trinotate_Annotation_Report
Downloaded 4 times
Description Metabetaeus minutus transcriptome annotation report containing output for putative ORFs from the various annotation methods used by the program Trinotate
Download Metabetaeus_minutus_Trinotate_Annotation_...14.tab (25.04 Mb)
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Title All_orthologous_clusters
Downloaded 34 times
Description A 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.
Download All_orthologous_clusters.zip (21.77 Mb)
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Title Filtered_subset_orthologous_clusters
Downloaded 36 times
Description A 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.
Download Filtered_subset_orthologous_clusters.zip (1.714 Mb)
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Title cd_hit_data
Downloaded 32 times
Description A 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.
Download cd_hit_data.zip (14.60 Mb)
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Title compliant_Fasta_files
Downloaded 36 times
Description A 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.
Download compliantFasta.zip (10.92 Mb)
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Title Remapping_expression
Downloaded 36 times
Description A 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.
Download Remapping_expression.zip (11.42 Mb)
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Title Assembly_script
Downloaded 4 times
Description This 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.
Download copy_concat_norm_TRI_hudAlpha_HISEQ2500.sh (1.459 Kb)
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Title Trinotate
Downloaded 13 times
Description This 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.
Download auto_Trinotate.sh (5.174 Kb)
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Title generate_Trinotate_report
Downloaded 10 times
Description This 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.
Download generate_Trinotate_report.sh (3.716 Kb)
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Title fasta_stats
Downloaded 8 times
Description This script will generate summary statistics from an assembled Trinity fasta file. See comments for usage, and if script is modified, please provide proper attribution.
Download fasta_stats.sh (304 bytes)
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Title Ortho1
Downloaded 10 times
Description This 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.
Download Ortho1.sh (1.642 Kb)
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Title Ortho2
Downloaded 7 times
Description This 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.
Download Ortho2.sh (400 bytes)
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Title clustalAlign
Downloaded 6 times
Description This 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.
Download clustalAlign.sh (612 bytes)
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Title Mapping
Downloaded 7 times
Description This 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.
Download Mapping.sh (726 bytes)
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When using this data, please cite the original publication:

Genomic Resources Development Consortium, Havird JC, Santos SR (2014) Genomic Resources Notes accepted 1 June 2014 - 31 July 2014. Molecular Ecology Resources 14(6): 1322. http://dx.doi.org/10.1111/1755-0998.12315

Additionally, please cite the Dryad data package:

Havird JC, Santos SR (2014) 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. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.jn8t1
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