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teachings:tuto_16s_microbial_analysis [2020/09/08 15:51] – olivier | teachings:tuto_16s_microbial_analysis [2022/10/13 14:12] (current) – olivier | ||
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* To know what a fasta or fastq (fastaq = fq) file is | * 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 ">" | + | 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 | + | |
- | </ | + | |
- | <nowiki> | + | //>human_T1 (UCSC April 2002 chr7: |
- | > | + | TTGTCAGATTCACCAAAGTTGAAATGAAGGAAAAAATGCTAAGGGCAGCC\\ |
- | ATACGACYCTTATTGTTAGTATATAATTTATATGAAAACMAAAAATTATG | + | AGAGAGAGGTCAGGTTACCCACAAAGGGAAGCCCATCAGACTAACAGCG\\ |
- | GCGGTATTTTAAGCTTTTCAGAGGAATTTGCTCTTTAATGGATAAAAC | + | ATCTCTCGGCAGAAACCCTACAGGCCAGAAGAGAGTGGGGGCCAATATT\\ |
- | CTAAATCTTACTAGAATTAGTAAAGCAGTTTGTATACCACT | + | CATATTCTTAAAGAAAAGAATTTTCAACCCAGAATTTCATATCCAGCCAA\\ |
- | </nowiki> | + | > |
+ | ATACGACYCTTATTGTTAGTATATAATTTATATGAAAACMAAAAATTATG\\ | ||
+ | GCGGTATTTTAAGCTTTTCAGAGGAATTTGCTCTTTAATGGATAAAAC\\ | ||
+ | CTAAATCTTACTAGAATTAGTAAAGCAGTTTGTATACCACT\\ \\ | ||
+ | // | ||
</ | </ | ||
\\ | \\ | ||
+ | * an access to a Galaxy website server, including usual tools for metagenomic analysis | ||
- | * an access to a Galaxy website server including usual tools for metagenomic analysis | + | See what is the Galaxy project: [[https:// |
- | + | ||
- | - 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 Galaxy servers are available. Here a list of servers including the required metaG tools (//list updated November 2022//): | ||
+ | |||
+ | https:// | ||
+ | https:// | ||
+ | https:// | ||
+ | https:// | ||
+ | https:// | ||
+ | https:// | ||
+ | https:// | ||
+ | https:// | ||
+ | https:// | ||
+ | https:// | ||
+ | https:// | ||
+ | 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: | ||
+ | |||
+ | < | ||
- | => 3 solutions: | + | 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). |
- | * Use a freely distant server | + | - Go here in your browser |
- | many servers are available, | + | |
- | | + | |
- | \\ \\ https://usegalaxy.org.au/ | + | |
+ | __pro__: fast server, depending of you computer power. Reusable.\\ | ||
+ | __cons__: harder (and long) to install. Take some disk space onto your hard drive. | ||
- | * Create an account on of these Galaxy server : * google it for others servers ! | + | -------- |
+ | then, | ||
+ | * Create a personal account into Galaxy (top-right menu) | ||
- | * => Start this tutorial : [[https:// | + | * Start this tutorial : [[http:// |