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teachings:tuto_16s_microbial_analysis [2020/02/06 14:10] – olivier | teachings:tuto_16s_microbial_analysis [2022/02/07 11:39] – olivier | ||
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==== 16S Microbial Analysis (with Galaxy) ==== | ==== 16S Microbial Analysis (with Galaxy) ==== | ||
- | This tutorial | + | __This |
- | * a computer (under Linux, Mac, Windows) with an internet connection | + | * a computer (under Linux, Mac, Windows) |
+ | |||
+ | * To know what a fasta or fastq (fastaq = fq) file is | ||
+ | < | ||
+ | Data in text format used to store nucleic acid sequences (such as DNA sequences) or protein sequences; may contain multiple sequences. FASTA files often start with a header line that may contain comments or other information. The rest of the file contains sequence data. Each sequence starts with a ">" | ||
- | | + | //> |
+ | TTGTCAGATTCACCAAAGTTGAAATGAAGGAAAAAATGCTAAGGGCAGCC\\ | ||
+ | AGAGAGAGGTCAGGTTACCCACAAAGGGAAGCCCATCAGACTAACAGCG\\ | ||
+ | ATCTCTCGGCAGAAACCCTACAGGCCAGAAGAGAGTGGGGGCCAATATT\\ | ||
+ | CATATTCTTAAAGAAAAGAATTTTCAACCCAGAATTTCATATCCAGCCAA\\ | ||
+ | > | ||
+ | ATACGACYCTTATTGTTAGTATATAATTTATATGAAAACMAAAAATTATG\\ | ||
+ | GCGGTATTTTAAGCTTTTCAGAGGAATTTGCTCTTTAATGGATAAAAC\\ | ||
+ | CTAAATCTTACTAGAATTAGTAAAGCAGTTTGTATACCACT\\ \\ | ||
+ | // | ||
+ | |||
+ | </ | ||
+ | \\ | ||
+ | | ||
+ | |||
+ | See what is the Galaxy project: [[https:// | ||
{{ : | {{ : | ||
+ | //Example of the main display page of Galaxy (using a browser)// | ||
+ | |||
+ | => __3 possibilities to get access to a Galaxy server__: | ||
+ | |||
+ | | ||
+ | |||
+ | Many public servers are available. Here a list of servers including metaG tools: | ||
+ | |||
+ | https:// | ||
+ | |||
+ | __pro__: no installation required, usable directly \\ | ||
+ | __cons__: some limitations and slow (or super slow) when running big computations | ||
+ | |||
+ | | ||
+ | |||
+ | | ||
+ | |||
+ | __pro__: no installation required, usable directly\\ | ||
+ | __cons__: should to be faster than previous servers, but depending the number of students connected at the same time ! | ||
+ | |||
+ | | ||
+ | |||
+ | - install " | ||
+ | - install a Galaxy server into Docker and run docker, by typing this single command: | ||
+ | |||
+ | < | ||
+ | |||
+ | Wait a loooong time before it starts : 5-10 Go to download the first time! => do it at home using a fast internet connection. Further starts are faster (re type the same command to enable the server). | ||
+ | |||
+ | - Go here in your browser : http:// | ||
- | * Create an account on of these Galaxy server : \\ \\ https:// | + | __pro__: fast server, depending |
+ | __cons__: harder (and long) to install. Take some disk space onto your hard drive. | ||
- | * To know what a fasta or fastq (fastaq = fq) file is : | + | -------- |
+ | then, | ||
- | //Data in text format used to store nucleic acid sequences (such as DNA sequences) or protein sequences; may contain multiple sequences. FASTA files often start with a header line that may contain comments or other information. The rest of the file contains sequence data. Each sequence starts with a ">" | ||
- | > | ||
- | TTGTCAGATTCACCAAAGTTGAAATGAAGGAAAAAATGCTAAGGGCAGCC | ||
- | AGAGAGAGGTCAGGTTACCCACAAAGGGAAGCCCATCAGACTAACAGCG | ||
- | ATCTCTCGGCAGAAACCCTACAGGCCAGAAGAGAGTGGGGGCCAATATT | ||
- | CATATTCTTAAAGAAAAGAATTTTCAACCCAGAATTTCATATCCAGCCAA | ||
- | </ | ||
- | < | + | * Create a personal account into Galaxy |
- | > | + | |
- | ATACGACYCTTATTGTTAGTATATAATTTATATGAAAACMAAAAATTATG | + | |
- | GCGGTATTTTAAGCTTTTCAGAGGAATTTGCTCTTTAATGGATAAAAC | + | |
- | CTAAATCTTACTAGAATTAGTAAAGCAGTTTGTATACCACT | + | |
- | </ | + | |
- | * Start this tutrorial | + | * Start this tutorial |