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You have already worked with a paired-end yeast ChIP-seq dataset, which we will continue to use here.  For the sake of uniformity, however, we will set up a new directory in your scratch area and copy over all called 'alignment' and fill it with our sequencing data.  To set up our areayour scratch area properly and move into it, execute something like:

Code Block
languagebash
title"Permanent" location for original data
mkdir $SCRATCH/alignment

We will also use two additional RNA-seq datasets, which are located at:

Code Block

cd $SCRATCH/alignment
mkdir fastq

Now you have created the alignment directory, moved into it, and created a subdirectory for our raw fastq files.  We will be using four data sets that consist of five files (since the paired-end data set has two separate files for each of the R1 and R2 reads).  To copy them over, execute something like:

Code Block
cd $SCRATCH/alignment/fastq
cp /corral-repl/utexas/BioITeam/core_ngs_tools/human_stuff/alignment/*fastq.gz .

We first moved ourselves into the fastq directory, then copied over all files that end in "fastq.gz" in the corral directory specified in the second line.  These are descriptions of the five files we copied:

File NameDescriptionSample
Sample_Yeast_L005_R1.cat.fastq.gzPaired-end Illumina, First of pair, FASTQYeast ChIP-seq
Sample_Yeast_L005_R2.cat.fastq.gzPaired-end Illumina, Second of pair, FASTQYeast ChIP-seq
human_rnaseq.fastq.gzPaired-end Illumina, First of pair only, FASTQHuman RNA-seq
human_mirnaseq.fastq.gzSingle-end Illumina, FASTQHuman microRNA-seq
cholera_rnaseq.fastq.gzSingle-end Illumina, FASTQV. cholerae RNA-seq

First copy the two human datasets to your $SCRATCH/core_ngs/fastq_prep directory.

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