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v4 May 2023

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ayushi-agrawal-gladstone 2023-05-11 15:06:17 -07:00
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intro-rna-seq/README.md
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[Link to wiki page](https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki/Introduction-to-RNA-Seq-Analysis)
### 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_session1.txt (text file with steps used on wynton to download/uplaod files, change directories etc in session 1)
- steps_on_wynton_session2.txt (text file with steps used on wynton to download/uplaod files, change directories etc in session 2)
- all_steps_docker_desktop.sh (shell script for running all the analysis steps using Docker Desktop and the practice data provided)
1. Single_read.fastq (fastq file with a single read to understand the fastq file format)
2. Bacteria_GATTACA_L001_R1_001.fastq (single-end small practice data with 100k reads for the demo in the workshop)
3. Adapter_Sequence.fasta (fasta file with adapter sequence for demo with cutadapt)
4. rDNA_sequence.fasta (fasta file with the reference genome sequence for demo with STAR aligner)
5. rDNA.gtf (GTF file with the annotations for demo with featureCounts)
6. all_steps_wynton.sh (shell script for running all the analysis steps on UCSF Wynton command-line interface using the practice data provided)
7. steps_on_wynton_part1.txt (text file with steps used on wynton to setup the folders, upload the data and create a singularity container)
8. steps_on_wynton_part2.txt (text file with steps used on wynton to run the bulk RNA-seq analysis using the demo files)
9. all_steps_docker_desktop.sh (shell script with commands for running all the analysis steps using Docker Desktop and the demo files)