MMG434
  • Install software and use FileZilla to transfer files
    • Software to install:
    • Using FileZilla to transfer files:
    • R
    • RStudio
    • Qualimap
    • Transferring files from your machine to the HPCC using FileZilla
  • RNA-seq background information, basic Linux/Unix commands, Trimmomatic, and FastQC
    • RNA-seq background information
    • Basic Linux/Unix commands
    • Getting some RNA-seq data
    • Trimmomatic
    • FastQC
    • Automating all of this
  • Align sequences with Bowtie and count gene features with HTSeq
    • Bowtie
    • HTSeq
  • Analyzing L. reuteri data
  • Modification to the scripts from today (3-4-15)!
  • Differential gene expression analysis with edgeR
    • Download and install edgeR
    • Read in the data to RStudio
    • Group the data together
    • Filter out low counts
    • Regroup and normalize the libraries
    • See how samples separate by treatment
    • Differential expression calculations
    • Plot the results
  • FastQC files
  • License
  • Questions?
 
MMG434
  • Docs »
  • FastQC files
  • Edit on GitHub

FastQC filesΒΆ

I hope you all had an excellent Spring Break! Here are all of the FastQC files to download for each sample.

LB Controls

  • trimmedLRLB1_fastqc.html
  • trimmedLRLB2_fastqc.html
  • trimmedLRLB3_fastqc.html
  • trimmedLRLB4_fastqc.html

Indole Treated

  • trimmedLRindole1_fastqc.html
  • trimmedLRindole2_fastqc.html
  • trimmedLRindole3_fastqc.html
  • trimmedLRindole4_fastqc.html
  • trimmedLRindole5_fastqc.html
  • trimmedLRindole6_fastqc.html

Commensal Conditioned Medium Treated

  • trimmedLRcomm1_fastqc.html
  • trimmedLRcomm2_fastqc.html
  • trimmedLRcomm3_fastqc.html
  • trimmedLRcomm4_fastqc.html
  • trimmedLRcomm5_fastqc.html
  • trimmedLRcomm6_fastqc.html
  • trimmedLRcomm7_fastqc.html

EHEC Conditioned Medium Treated

  • trimmedLRehec1_fastqc.html
  • trimmedLRehec2_fastqc.html
  • trimmedLRehec3_fastqc.html
  • trimmedLRehec4_fastqc.html
  • trimmedLRehec5_fastqc.html
  • trimmedLRehec6_fastqc.html
  • trimmedLRehec7_fastqc.html
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