Data from: Plasticity in gene transcription explains the differential performance of two invasive fish species

Wellband KW, Heath DD

Date Published: January 31, 2017

DOI: https://doi.org/10.5061/dryad.408ht

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Title Round goby transcript count data
Downloaded 2 times
Description This file was generated using Corset software to process BAM files of RNAseq reads mapped to a de novo assembled transcriptome for nine round goby and enumerate counts of reads per transcript as a proxy for transcript abundance.
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Title Tubenose goby transcript count data
Downloaded 3 times
Description This file was generated using Corset software to process BAM files of RNAseq reads mapped to a de novo assembled transcriptome for nine tubenose goby and enumerate counts of reads per transcript as a proxy for transcript abundance.
Download TNG_counts.txt (2.350 Mb)
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Title R code for round goby differential expression analysis
Downloaded 4 times
Download RG_analysis.R (3.108 Kb)
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Title R code for tubenose goby differential expression analysis
Downloaded 7 times
Download TNG_analysis.R (3.133 Kb)
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Title R code for analysis of shared orthologs
Downloaded 4 times
Description This R code uses information about the reciprocal best BLAST matches between round and tubenose goby transcripts to combine and analyze the count datasets for shared orthologs.
Download RG_TNG_comparision.R (6.573 Kb)
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Title Reciprocal best hits between round and tubenose goby transcripts
Downloaded 4 times
Description This file was generated by reciprocally BLASTing the translated longest open reading frame of one species on the other. Pairs of round and tubenose goby transcripts retained in this file are where the pair represent each others best match. This file is required for the analysis of shared orthologs.
Download RBH_blastp_with_masking_and_sw.txt (746.2 Kb)
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Title Unix shell script for transcriptome assembly and read mapping
Downloaded 8 times
Description This script was used to perform de novo transcriptome assembly and read mapping for both round and tubenose goby. Its inclusion is primarily to document specific parameters used for these analysis steps.
Download goby_transcriptomics_unix_code.txt (2.047 Kb)
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When using this data, please cite the original publication:

Wellband KW, Heath DD (2017) Plasticity in gene transcription explains the differential performance of two invasive fish species. Evolutionary Applications 10(6): 563–576. https://doi.org/10.1111/eva.12463

Additionally, please cite the Dryad data package:

Wellband KW, Heath DD (2017) Data from: Plasticity in gene transcription explains the differential performance of two invasive fish species. Dryad Digital Repository. https://doi.org/10.5061/dryad.408ht
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