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Update wolf_tutorial

Celine Mercier
2019-03-31 15:29:20 +02:00
parent 2d50a33e84
commit 45242cbc7a
1 changed files with 36 additions and 7 deletions
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wolf_tutorial.md

@ -26,7 +26,9 @@ The new database system used by the OBITools3 (called **DMS** for Data Managemen
Any hybrid of those 2 works too. Any hybrid of those 2 works too.
**Note:** View names must be unique within a DMS, in other words, views can not be overwritten. * View names must be unique within a DMS, in other words, views can not be overwritten.
* All tools accept different input and output DMS.
* If the output DMS is not given, the input DMS is used. * If the output DMS is not given, the input DMS is used.
@ -39,6 +41,12 @@ The new database system used by the OBITools3 (called **DMS** for Data Managemen
* `obi command -h` prints the help of the command. * `obi command -h` prints the help of the command.
### 0.3 Before starting: installing the OBITools3
Not working yet...
### 1. Import the sequencing data in a DMS ### 1. Import the sequencing data in a DMS
1. Import the first set of reads, with : 1. Import the first set of reads, with :
@ -120,6 +128,8 @@ Unlike the OBITools1, the OBITools3 make it possible to run ngsfilter before ali
For EMBL files, you can give the path to a directory with several EMBL files. For EMBL files, you can give the path to a directory with several EMBL files.
**Note:** The reference database can be built in another DMS.
3. Download the taxonomy: 3. Download the taxonomy:
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
@ -140,7 +150,7 @@ For EMBL files, you can give the path to a directory with several EMBL files.
2. Build the reference database specifically used by the OBITools3 to make ecotag efficient: 2. Build the reference database specifically used by the OBITools3 to make ecotag efficient:
obi build_ref_db --taxonomy wolf/taxonomy/my_tax wolf/v05_db_clean wolf/v05_db_definitive obi build_ref_db -t 0.95 --taxonomy wolf/taxonomy/my_tax wolf/v05_db_clean wolf/v05_db_definitive
#### Assign each sequence to a taxon #### Assign each sequence to a taxon
@ -161,9 +171,28 @@ For example:
obi align -t 0.95 wolf/assigned_sequences wolf/aligned_assigned_sequences obi align -t 0.95 wolf/assigned_sequences wolf/aligned_assigned_sequences
#### Check the history of everything that was done #### Check the history of everything that was done
obi history
The default history is in bash:
obi history wolf
The most visual way to look at the pipeline is:
obi history -d wolf > wolf.dot
obi history -d wolf/cleaned_sequences > wolf_one_view.dot
To look at the graph produced, open the dot file:
dot -Tx11 wolf.dot
or convert the dot file to a png image file:
dot -Tpng wolf.dot -o wolf.png
open wolf.png &
You will get something like this:
![wolf](/uploads/7cb6d08cd5c645ee20ac49d233d2dc9a/wolf.png)
#### Export the results #### Export the results
@ -171,10 +200,10 @@ Export in fasta format:
obi export --fasta-output wolf/assigned_sequences wolf_results.fasta obi export --fasta-output wolf/assigned_sequences wolf_results.fasta
Export in csv-like format (very soon to be implemented :)): Export in csv-like format:
obi export --tab-output wolf/assigned_sequences wolf_results.fasta obi export --tab-output wolf/aligned_assigned_sequences wolf_results.csv
### Contact ### Contact
<celine.mercier@metabarcoding.org> <celine.mercier@metabarcoding.org>