Page Comparison

IF YOU HAVE YOUR OWN DATA:

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1. 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.

   Code Block
   title Get the data
   cds cd my_rnaseq_course cp -r /work2/projects/BioITeam/projects/courses/rnaseq_course/day_4_bottomley_raw_data . &

   
   

2. 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.
   
   

   Code Block
   title Get the data
   cds cd my_rnaseq_course cp -r /work2/projects/BioITeam/projects/courses/rnaseq_course/day_4_bottomley_mapped_data . &

   
   

3. 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.

   Code Block
   title Get the data
   cds cd my_rnaseq_course cp -r /work2/projects/BioITeam/projects/courses/rnaseq_course/day_4_brooks_gene_count_data . &

   
   

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