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You have already worked with a paired-end yeast ChIP-seq dataset, which we will continue to use here. We will also use two additional RNA-seq datasets. The additional data are located in the path:
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/corral-repl/utexas/BioITeam$SCRATCH/core_ngs_tools/human_stuff |
So, the following are the data files you will need:
| File Name | Description | Sample |
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| 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 |
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 "
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cds
mkdir raw_data
cp /corral-repl/utexas/BioITeam/core_ngs_tools/*/*.fastq.gz ./raw_data/
cd raw_data/ |
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Do you believe that I gave you files of any reasonable quality? I wouldn't, so you should check it outDo a fast quality check on the two new data files like you did earlier on the yeast files.
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cds; cd raw_data
module load fastqc
fastqc human_rnaseq.fastq.gz
fastqc human_mirnaseq.fastq.gz |
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