Skip to content
Projects
Groups
Snippets
Help
This project
Loading...
Sign in / Register
Toggle navigation
O
OBITools
Overview
Overview
Details
Activity
Cycle Analytics
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
Charts
Issues
26
Issues
26
List
Board
Labels
Milestones
Merge Requests
0
Merge Requests
0
Wiki
Wiki
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Charts
Create a new issue
Commits
Issue Boards
Open sidebar
OBITools
OBITools
Commits
713d621d
Commit
713d621d
authored
Feb 13, 2014
by
Eric Coissac
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
--no commit message
parent
ad0b4e17
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
10 additions
and
9 deletions
+10
-9
wolves.rst
doc/sphinx/source/wolves.rst
+10
-9
No files found.
doc/sphinx/source/wolves.rst
View file @
713d621d
...
...
@@ -17,13 +17,13 @@ How to analyze DNA metabarcoding data produced on Illumina sequencers using:
| use : |
| |
| - :doc:`obicount <scripts/obicount>` to count for the number|
|
of sequence records in a file
|
|
of sequence records in a file
|
| - :doc:`obihead <scripts/obihead>` and |
|
:doc:`obitail <scripts/obitail>` to view the first
|
|
or last sequence records of a file
|
| - :doc:`obistat
obistat` to get some basic statistics (count,
|
|
mean, standard deviation) on the attributes
|
|
(key=value couples) in the fasta header of each
|
|
:doc:`obitail <scripts/obitail>` to view the first
|
|
or last sequence records of a file
|
| - :doc:`obistat
<scripts/obistat>` to get some basic
|
|
statistics (count, mean, standard deviation) on the
|
|
attributes (key=value couples) in the fasta header of each
|
| sequence record (see The `extended OBITools fasta format` |
| in the :doc:`fasta format <fasta>` description) |
| - any *Unix* command such as ``less``, ``awk``, ``sort``, |
...
...
@@ -47,12 +47,12 @@ The data needed to run the tutorial are the following:
- the file describing the primers and tags used for all samples sequenced:
* ``wolf_ngsfilter.txt``
The tags correspond to short and specific sequences added on the 5' end of each primer to distinguish the different samples
The tags correspond to short and specific sequences added on the 5' end of each primer to distinguish the different samples
- the file containing the reference database in fasta format:
* ``db_v05_r117.fasta``
This reference database has been extracted from the release 117 of EMBL using :doc:`ecoPCR <scripts/ecoPCR>`
This reference database has been extracted from the release 117 of EMBL using :doc:`ecoPCR <scripts/ecoPCR>`
- the NCBI taxonomy formatted in the :doc:`ecoPCR <scripts/ecoPCR>` format (see the :doc:`obiconvert <scripts/obiconvert>` utility for details) :
...
...
@@ -191,7 +191,7 @@ it is convenient to work with uniq *sequences* instead of *reads*. To *dereplica
| 2. group strictly identical reads together |
| 3. output the sequence for each group and its count in the |
| original dataset (in this way, all duplicated reads are |
| removed) |
| removed)
|
| |
| Definition adapted from [#]_ |
+-------------------------------------------------------------+
...
...
@@ -225,6 +225,7 @@ The first sequence record of ``wolf.ali.ngs.uniq.fasta`` is:
The run of :doc:`obiuniq <scripts/obiuniq>` has added two key=values entries in the header of the fasta sequence :
- :py:mod:`merged_sample={'29a_F260619': 1}` : this sequence have been found once in a single sample
- :py:mod:`count=1` : the total number of counts for this sequence is 1
To keep only these two ``key=value`` informations, we can use the :doc:`obiannotate <scripts/obiannotate>` command:
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment