IF YOU HAVE YOUR OWN DATA:
- Make sure data is on stampede2 and in your scratch directory
- Make sure genome/transcriptome files are on stampede2 and in your scratch directory. If you need to download reference files, some options include:
- Make sure the files are readable
IF YOU DON'T HAVE YOUR OWN DATA:
You have several choices for datasets to play with, depending on the stage in the analysis that you would like to work on.
RAW DATA: Start with 6 raw fastq files from the following dataset:
Bottomley et Al mouse dataset SRA026846.1 (http://dx.doi.org/10.1371/journal.pone.0017820)
Single end RNA-Seq data generated on Illumina GAIIx for 2 strains of mice (B6 and D2) to detect differential striatal gene expression between the two nbred mouse strains.
We have provided three B6 and three D2 fastq files for you to work with.Get the datacds cd my_rnaseq_course cp -r /work2/projects/BioITeam/projects/courses/rnaseq_course/day_4_bottomley_raw_data . &
MAPPED FILES: Start with 6 bam files (mapped to the mouse MM9 genome) from the following dataset:
Bottomley et Al mouse dataset SRA026846.1 (http://dx.doi.org/10.1371/journal.pone.0017820)
Single end RNA-Seq data generated on Illumina GAIIx for 2 strains of mice (B6 and D2) to detect differential striatal gene expression between the two nbred mouse strains.
We have provided three B6 and three D2 fastq files for you to work with.Get the datacds cd my_rnaseq_course cp -r /work2/projects/BioITeam/projects/courses/rnaseq_course/day_4_bottomley_mapped_data . &
GENE COUNT DATA: Start with a table providing per-gene read counts for 3 treated and 4 untreatead Drosophila samples. From the following dataset:
Brooks et al, 2011 dataset GSE18508 (PMID: 20921232)
The experiment studied the effects of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. Treated samples have been RNAi depleted of mRNAs encoding RNA binding proteins and untreated samples have not.Get the datacds cd my_rnaseq_course cp -r /work2/projects/BioITeam/projects/courses/rnaseq_course/day_4_brooks_gene_count_data . &
REMINDERS
How to request an interactive session in one of stampede's compute nodes?
idev -m 120 -q normal -A UT-2015-05-18 -r RNAday5 (OR) idev -m 120 -q development -A UT-2015-05-18 #saay no when it asks if you wanted to use the reservation
How to submit jobs? Submitting Jobs to Stampede2
How to submit jobs in a sequence?
You can create a job that is dependent on another job finishing only start after the first job has completed using this command:
sbatch --dependency=afterok:<job-ID> launcher.slurm
|
How to move files between your computer and stampeded2: