Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Now we need to set up the raw data for processing. Stage these files on Stampede from Corral in the fewest possible commands .in a directly called "

Expand
titleHint:
Code Block
cds
mkdir raw_data
cp /corral-repl/utexas/BioITeam/core_ngs_tools/human_stuff*/*rnaseq* ..fastq.gz ./raw_data/
cd raw_data/

Do you believe that I gave you files of any reasonable quality?  I wouldn't, so you should check it out.

Expand
titleHint:
Code Block
 cds; cd raw_data
module load fastqc
fastqc human_rnaseq.fastq.gz
fastqc human_mirnaseq.fastq.gz

BWA - Yeast ChIP-seq

 

Bowtie2 and Local Alignment - Human microRNA-seq

...