From 45242cbc7a4a27109781a38a6fa46cd025b012ad Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Sun, 31 Mar 2019 15:29:20 +0200 Subject: [PATCH] Update wolf_tutorial --- wolf_tutorial.md | 43 ++++++++++++++++++++++++++++++++++++------- 1 file changed, 36 insertions(+), 7 deletions(-) diff --git a/wolf_tutorial.md b/wolf_tutorial.md index 275f1b4..2577aab 100644 --- a/wolf_tutorial.md +++ b/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. - **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. @@ -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. + +### 0.3 Before starting: installing the OBITools3 + +Not working yet... + + ### 1. Import the sequencing data in a DMS 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. +**Note:** The reference database can be built in another DMS. + 3. Download the taxonomy: 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: - 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 @@ -161,9 +171,28 @@ For example: obi align -t 0.95 wolf/assigned_sequences wolf/aligned_assigned_sequences #### 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 @@ -171,10 +200,10 @@ Export in fasta format: 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 - + \ No newline at end of file