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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:
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mkdir $SCRATCH/alignment |
We will also use two additional RNA-seq datasets, which are located at:
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:
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cd $SCRATCH/alignment/fastq
cp |
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/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 Name | Description | Sample |
|---|---|---|
| Sample_Yeast_L005_R1.cat.fastq.gz | Paired-end Illumina, First of pair, FASTQ | Yeast ChIP-seq |
| Sample_Yeast_L005_R2.cat.fastq.gz | Paired-end Illumina, Second of pair, FASTQ | Yeast ChIP-seq |
| human_rnaseq.fastq.gz | Paired-end Illumina, First of pair only, FASTQ | Human RNA-seq |
| human_mirnaseq.fastq.gz | Single-end Illumina, FASTQ | Human microRNA-seq |
| cholera_rnaseq.fastq.gz | Single-end Illumina, FASTQ | V. cholerae RNA-seq |
First copy the two human datasets to your $SCRATCH/core_ngs/fastq_prep directory.
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