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ayushi.agrawal aec4031f89 intro rna-seq fall 23
2023-09-15 11:53:35 -07:00
..
Adapter_Sequence.fasta First commit 2020-03-20 12:31:00 -07:00
all_steps_docker_desktop.sh Add files via upload 2022-07-13 16:09:25 -07:00
all_steps_docker_desktop_mac.sh commands for windows 2023-05-14 20:52:15 -07:00
all_steps_docker_desktop_windows.sh commands for windows 2023-05-14 20:52:15 -07:00
all_steps_wynton.sh Add files via upload 2022-07-13 16:09:25 -07:00
Bacteria_GATTACA_L001_R1_001.fastq added example files RNA-Seq 2019-12-06 10:59:25 -08:00
Intro_to_RNA-seq_data_analysis.zip intro rna-seq fall 23 2023-09-15 11:53:35 -07:00
rDNA.gtf First commit 2020-03-20 12:31:00 -07:00
rDNA_sequence.fasta added example files RNA-Seq 2019-12-06 10:59:25 -08:00
README.md commands for windows 2023-05-14 20:52:15 -07:00
Single_read.fastq added example files RNA-Seq 2019-12-06 10:59:25 -08:00
steps_on_wynton_part1.txt v4 May 2023 2023-05-11 15:06:17 -07:00
steps_on_wynton_part2.txt v4 May 2023 2023-05-11 15:06:17 -07:00
Workshop_FALL_2023 Introduction_to_RNA-seq_analysis-Michela_and_Ayushi.pptx intro rna-seq fall 23 2023-09-15 11:53:35 -07:00
Workshop_FALL_2023_Introduction_to_RNA-seq_analysis_Michela_and_Ayushi.pdf intro rna-seq fall 23 2023-09-15 11:53:35 -07:00

README.md

intro-rna-seq

Link to wiki page

Description of files

  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_mac.sh (commands for running all the analysis steps using Docker Desktop and the demo files on MacOS)
  10. all_steps_docker_desktop_windows.sh (commands for running all the analysis steps using Docker Desktop and the demo files on Windows)