v4 May 2023

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)
+1. 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)
+2. 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)
+3. 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)
+4. 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)
+5. 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)
+6. 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)
+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)
-- steps_on_wynton_session2.txt (text file with steps used on wynton to download/uplaod files, change directories etc in session 2)
+8. 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 for running all the analysis steps using Docker Desktop and the practice data provided)
+9. all_steps_docker_desktop.sh (shell script with commands for running all the analysis steps using Docker Desktop and the demo files)

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 ~
+#list the contents of the home directory or ~
-#the uploaded folder Intro_to_RNA-seq_data_analysis shoudl appear in the result
+#the uploaded folder Intro_to_RNA-seq_data_analysis should appear in the result
 [alice@log2 ~]$ ls
 
 #login to the development node