From fb44b310336a55776582690634111b5efb5bcfea Mon Sep 17 00:00:00 2001 From: nkleinbo Date: Fri, 20 Sep 2019 15:33:41 +0200 Subject: [PATCH] Update inspect_h5.rst --- docs/basecalling/inspect_h5.rst | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/docs/basecalling/inspect_h5.rst b/docs/basecalling/inspect_h5.rst index 0691fd5..04cd16c 100644 --- a/docs/basecalling/inspect_h5.rst +++ b/docs/basecalling/inspect_h5.rst @@ -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:: @@ -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:: @@ -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::