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| 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 |
Reference Genomes
Before we get to alignment, we need a genome to align to. We will use four different references here:
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| Reference | Species | Base Length | Contig Number | Source | Download |
|---|---|---|---|---|---|
| hg19 | Human | 3.1 Gbp | 25 (really 93) | UCSC | UCSC GoldenPath |
| sacCer3 | Yeast | 12.2 Mbp | 17 | UCSC | UCSC GoldenPath |
| mirbase V20 | Human | 160 Kbp | 1908 | Mirbase | Mirbase Downloads |
| vibCho (O395) | V. cholerae | ~4 Mbp | 2 | GenBank | GenBank Downloads |
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| Expand | ||
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| Recall that these are 100 bp reads and we did not remove adapter contamination. There will be a distribution of fragment sizes – some will be short – and those short fragments may not align without adapter removal (fastx_trimmer or cutadapt). |
Exercise #2: Bowtie2 - Vibrio
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cholerae RNA-seq
While we have focused on aligning eukaryotic data, the same tools can be used to perform identical functions with prokaryotic data. The major differences are less about the underlying data and much more about the external/public databases established to store and distribute reference data. For example, the Illumina iGenome resource provides pre-processed and uniform reference data, designed to be out-of-the-box compatible with aligners like bowtie2 and bwa. However, the limited number of available species are heavily biased towards model eukaryotes. If we wanted to study a prokaryote, the reference data must be downloaded from a resource like GenBank, and processed/indexed similarly to the procedure for mirbase.
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