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Update inspect_h5.rst
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nkleinbo committed Sep 20, 2019
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8 changes: 7 additions & 1 deletion docs/basecalling/inspect_h5.rst
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Expand Up @@ -54,6 +54,8 @@ Which you can simply count to get the number of reads in your fast5 file::
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/GXB01322_20181217_FAK35493_GA10000_sequencing_run_Run00014_MIN106_RBK004_46674_0.fast5/read_a3d14887-0d45-4ef5-8a20-42af8257053d
or (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::
Expand All @@ -66,6 +68,8 @@ 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/GXB01322_20181217_FAK35493_GA10000_sequencing_run_Run00014_MIN106_RBK004_46674_0.fast5/read_a3d14887-0d45-4ef5-8a20-42af8257053d/Raw
or (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::
Expand All @@ -74,7 +78,9 @@ 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/GXB01322_20181217_FAK35493_GA10000_sequencing_run_Run00014_MIN106_RBK004_46674_0.fast5/read_0061d165-af04-4c39-ad5e-8c4ebe3caa80/Raw/Signal
h5ls data/fast5_tiny/GXB01322_20181217_FAK35493_GA10000_sequencing_run_Run00014_MIN106_RBK004_46674_0.fast5/read_a3d14887-0d45-4ef5-8a20-42af8257053d/Raw/Signal
or (group2):
h5ls 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::

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