Scripts and data for speedy analysis of SCTLD transcriptomes from several Caribbean coral species.
These transcriptomes were obtained for species both with and without reference genomes and transcriptomes, so two different sequencing methodologies were employed. Separate directores for each approach (RNAseq/TagSeq) contain the associated sample metadata, analysis scripts and pipeline outputs.
Helpful slides higlighting difference between TagSeq and standard RNAseq: https://ucdavis-bioinformatics-training.github.io/2017-June-RNA-Seq-Workshop/wednesday/TagSeqVSRnaSeq.pdf
Scripts for general TagSeq analyses provided by Matz Lab at UT Arlington: https://github.com/z0on/tag-based_RNAseq
Montastrea cavernosa Genome resources from the Matz lab: https://matzlab.weebly.com/data--code.html
Orbicella faveolata Genome resources from the NCBI: https://www.ncbi.nlm.nih.gov/assembly/GCF_002042975.1/
Pseudodiploria clivosa Paper on immunotranscriptome of P. strigosa:
Colpophyllia natans De novo transcriptome assembly: https://github.com/trinityrnaseq/trinityrnaseq/wiki Annotation of de novo transcriptome: https://github.com/z0on/annotatingTranscriptomes TransDecoder software guide: https://github.com/TransDecoder/TransDecoder/wiki Trinotate pipeline: https://github.com/Trinotate egg-NOG-mapper: http://eggnog-mapper.embl.de/