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| .. | ||
| Adapter_Sequence.fasta | ||
| all_steps_docker_desktop.sh | ||
| all_steps_wynton.sh | ||
| Bacteria_GATTACA_L001_R1_001.fastq | ||
| Intro_to_RNA-seq_data_analysis.zip | ||
| rDNA.gtf | ||
| rDNA_sequence.fasta | ||
| README.md | ||
| Single_read.fastq | ||
| steps_on_wynton_part1.txt | ||
| steps_on_wynton_part2.txt | ||
| Workshop_May2023_Intro_to_RNA-seq_analysis-Michela_and_Ayushi.pptx | ||
intro-rna-seq
Description of files
- Single_read.fastq (fastq file with a single read to understand the fastq file format)
- Bacteria_GATTACA_L001_R1_001.fastq (single-end small practice data with 100k reads for the demo in the workshop)
- Adapter_Sequence.fasta (fasta file with adapter sequence for demo with cutadapt)
- rDNA_sequence.fasta (fasta file with the reference genome sequence for demo with STAR aligner)
- rDNA.gtf (GTF file with the annotations for demo with featureCounts)
- all_steps_wynton.sh (shell script for running all the analysis steps on UCSF Wynton command-line interface using the practice data provided)
- steps_on_wynton_part1.txt (text file with steps used on wynton to setup the folders, upload the data and create a singularity container)
- steps_on_wynton_part2.txt (text file with steps used on wynton to run the bulk RNA-seq analysis using the demo files)
- all_steps_docker_desktop.sh (shell script with commands for running all the analysis steps using Docker Desktop and the demo files)