getting our metagenomic datasets - AstrobioMike/JPL-HBCU-2020 GitHub Wiki
We will be working with 8 sample datasets of metagenomic reads. Illumina sequencing is often done as paired-end sequencing, which is the case for these datasets. This means there is a "forward" and "reverse" read file for each sample (commonly designated as "R1" and "R2" as below). So there are in total 16 files for our 8 samples. Additionally, the files also have "trimmed" in their names because the initial "raw" sequencing files have been processed with a tool called Trimmomatic which performs trimming and filtering of reads based on their quality scores.
These can be downloaded to our instances and unpacked with the following commands (they are ~5 GB in total):
curl -L -o metagenomic-read-files.tar.gz https://ndownloader.figshare.com/files/24079451
tar -xzvf metagenomic-read-files.tar.gz| Sample | Associated files |
|---|---|
| Sample 1 | sample1_R1_trimmed.fastq.gz sample1_R2_trimmed.fastq.gz |
| Sample 2 | sample2_R1_trimmed.fastq.gz sample2_R2_trimmed.fastq.gz |
| Sample 3 | sample3_R1_trimmed.fastq.gz sample3_R2_trimmed.fastq.gz |
| Sample 4 | sample4_R1_trimmed.fastq.gz sample4_R2_trimmed.fastq.gz |
| Sample 5 | sample5_R1_trimmed.fastq.gz sample5_R2_trimmed.fastq.gz |
| Sample 6 | sample6_R1_trimmed.fastq.gz sample6_R2_trimmed.fastq.gz |
| Sample 7 | sample7_R1_trimmed.fastq.gz sample7_R2_trimmed.fastq.gz |
| Sample 8 | sample8_R1_trimmed.fastq.gz sample8_R2_trimmed.fastq.gz |