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Removing docs of preview mode
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isaacovercast committed Jul 27, 2018
1 parent 517d83f commit b3ad7ba
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11 changes: 4 additions & 7 deletions docs/pedicularis_cli.rst
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Expand Up @@ -172,15 +172,13 @@ simply branching "base" again with a different list of Samples.
41954_cyathophylloides 1 2199613
**Subsampling data**:
A special flag (--preview) can be called during step2 to subsample a specific
number of reads per Sample. The default is 100K reads, which in this case
is about 5-10% of the total. This will make our analysis run very fast downstream.
**Running step 2**:


.. code:: bash
## run step2 in preview mode
>>> ipyrad -p params-sub4.txt -s 2 --preview -r
## run step2
>>> ipyrad -p params-sub4.txt -s 2 -r
.. parsed-literal::
Expand All @@ -193,7 +191,6 @@ is about 5-10% of the total. This will make our analysis run very fast downstrea
ipyparallel setup: Local connection to 4 Engines
Step2: Filtering reads
Running preview mode: subselecting maximum of 100000 reads per sample
[####################] 100% processing reads | 0:02:48
Saving Assembly.
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1 change: 0 additions & 1 deletion docs/test_rad.rst
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Expand Up @@ -193,7 +193,6 @@ Assembly object name.
.. code:: python
## run step 3 to cluster reads within samples using vsearch
#data1.step3(['2E_0'], force=True, preview=True) # ["2H_0", "2G_0"])
data1.step3(force=True)
## print the results
print data1.stats.head()
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