Update inspect_h5.rst

metagenomics · Sep 20, 2019 · 8c01b4a · 8c01b4a
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diff --git a/docs/basecalling/inspect_h5.rst b/docs/basecalling/inspect_h5.rst
@@ -10,8 +10,6 @@ The HDF5 tools can be used to display contents of HDF5 files. We will use two of
   
 In order to get the complete content of a fast5 in readable form, you can use::
 
-  h5dump data/fast5_tiny/XXX.fast5 | more
-  or for group2:
   h5dump data/fast5_tiny/GXB01322_20181217_FAK35493_GA10000_sequencing_run_Run00014_MIN106_RBK004_46674_0.fast5 | more
 
 Inspect the output. The file starts with a root group::
@@ -36,8 +34,6 @@ at some point, the actual data is stored as a dataset::
   
 To get an overview on all reads, you could use the h5ls command::
 
-  h5ls data/fast5_tiny/XXX.fast5 
-  or for group2:
   h5ls data/fast5_tiny/GXB01322_20181217_FAK35493_GA10000_sequencing_run_Run00014_MIN106_RBK004_46674_0.fast5
   
 This will give you a list of all reads::
@@ -54,14 +50,10 @@ This will give you a list of all reads::
 
 Which you can simply count to get the number of reads in your fast5 file::
   
-  h5ls data/fast5_tiny/XXX.fast5 | wc -l
-  or for group2:
   h5ls data/fast5_tiny/GXB01322_20181217_FAK35493_GA10000_sequencing_run_Run00014_MIN106_RBK004_46674_0.fast5 | wc -l 
     
 In order to inspect what is stored for an individual read, you can specify that read, as if it were a directory using h5ls::
 
-  h5ls data/fast5_tiny/XXX.fast5/YYY
-  or for group2:
   h5ls data/fast5_tiny/GXB01322_20181217_FAK35493_GA10000_sequencing_run_Run00014_MIN106_RBK004_46674_0.fast5/read_0061d165-af04-4c39-ad5e-8c4ebe3caa80
   
 Which gives you the groups ("subdirectories") for that Read::
@@ -74,8 +66,6 @@ Which gives you the groups ("subdirectories") for that Read::
   
 Let's assume, we are interested in the raw data of a specific read::
 
-  h5ls data/fast5_tiny/XXX.fast5/YYY/Raw
-  or for group2:
   h5ls data/fast5_tiny/GXB01322_20181217_FAK35493_GA10000_sequencing_run_Run00014_MIN106_RBK004_46674_0.fast5/read_0061d165-af04-4c39-ad5e-8c4ebe3caa80/Raw
   
 The output is::
@@ -84,8 +74,6 @@ The output is::
   
 So we have reached the actual raw data (indicated by "Dataset"). To view a dataset, h5ls has a '-d' option::
 
-  h5ls -d data/fast5_tiny/XXX.fast5/YYY/Raw/Signal
-  or for group2:
   h5ls -d data/fast5_tiny/GXB01322_20181217_FAK35493_GA10000_sequencing_run_Run00014_MIN106_RBK004_46674_0.fast5/read_0061d165-af04-4c39-ad5e-8c4ebe3caa80/Raw/Signal
   
 Which will give you the raw signal of that specific read::
@@ -109,4 +97,3 @@ References
 ^^^^^^^^^^
 
 **HDF5 tools** https://support.hdfgroup.org/products/hdf5_tools/
-