├── .gitignore ├── 01_raw_data ├── 01_fasterq_dump.sh ├── 02_get_genome.sh ├── accessionlist.txt └── metadata.txt ├── 02_quality_control ├── 01_fastp_trim.sh ├── 02_fastqc.sh └── 03_multiqc.sh ├── 03_index └── hisat2_index.sh ├── 04_align └── align.sh ├── 05_align_qc ├── 01_samtools_stats.sh ├── 02_qualimap.sh └── 03_multiqc.sh ├── 06_count └── htseq_count.sh ├── 07_stringtie ├── 01_stringtie_assemble.sh ├── 02_stringie_merge.sh └── 03_gtf_annotate.sh ├── 08_kallisto ├── 01_kallisto_stringtie.sh └── 02_kallisto_ensembl.sh ├── LICENSE ├── README.md ├── images ├── Croaker_DESeq2-HEATMAP.png ├── Croaker_DESeq2-MAplot_initial_analysis.png ├── Croaker_DESeq2-clustering.png ├── Croaker_DESeq2-ggplot2.png ├── fastqc1.png ├── fastqc2.png ├── fastqc3.png ├── fastqc4.png ├── heatmap1.jpg ├── heatmap2.jpg ├── heatmap3.jpg └── killi_pca.png ├── r_analysis ├── DE_analysis_htseq.R └── r_intro.R └── setup.sh /.gitignore: -------------------------------------------------------------------------------- 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