diff --git a/intro-rna-seq/Intro_to_RNA-seq_data_analysis.zip b/intro-rna-seq/Intro_to_RNA-seq_data_analysis.zip index aef55bc..238409d 100644 Binary files a/intro-rna-seq/Intro_to_RNA-seq_data_analysis.zip and b/intro-rna-seq/Intro_to_RNA-seq_data_analysis.zip differ diff --git a/intro-rna-seq/README.md b/intro-rna-seq/README.md index d321b56..ca76e48 100644 --- a/intro-rna-seq/README.md +++ b/intro-rna-seq/README.md @@ -2,12 +2,12 @@ [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) diff --git a/intro-rna-seq/Workshop_2022_ Introduction to RNA-seq analysis - Michela and Ayushi .pptx b/intro-rna-seq/Workshop_2022_ Introduction to RNA-seq analysis - Michela and Ayushi .pptx deleted file mode 100644 index 486a043..0000000 Binary files a/intro-rna-seq/Workshop_2022_ Introduction to RNA-seq analysis - Michela and Ayushi .pptx and /dev/null differ diff --git a/intro-rna-seq/steps_on_wynton_session1.txt b/intro-rna-seq/steps_on_wynton_part1.txt similarity index 95% rename from intro-rna-seq/steps_on_wynton_session1.txt rename to intro-rna-seq/steps_on_wynton_part1.txt index 809bbb5..f0b47a2 100644 --- a/intro-rna-seq/steps_on_wynton_session1.txt +++ b/intro-rna-seq/steps_on_wynton_part1.txt @@ -9,8 +9,8 @@ #enter your wynton password when prompted and hit enter #once you are logged in to wynton, -#list the contents of the home diretory or ~ -#the uploaded folder Intro_to_RNA-seq_data_analysis shoudl appear in the result +#list the contents of the home directory or ~ +#the uploaded folder Intro_to_RNA-seq_data_analysis should appear in the result [alice@log2 ~]$ ls #login to the development node diff --git a/intro-rna-seq/steps_on_wynton_session2.txt b/intro-rna-seq/steps_on_wynton_part2.txt similarity index 100% rename from intro-rna-seq/steps_on_wynton_session2.txt rename to intro-rna-seq/steps_on_wynton_part2.txt