Update and expand tutorials against real ENCODE data

README.md

@@ -3,7 +3,7 @@
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 [![PyPIDownloadsTotal](https://pepy.tech/badge/isotools)](https://pepy.tech/project/isotools)
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-<img align="right" src="https://raw.githubusercontent.com/HerwigLab/IsoTools2/master/IsoToolsLogo.png" alt="IsoTools Logo" width="300"  />
+<img align="right" src="https://raw.githubusercontent.com/HerwigLab/IsoTools2/master/IsoToolsLogo.png" alt="IsoTools Logo" width="150"  />
 
 # IsoTools
 

docs/notebooks/01_prepare_data.ipynb

@@ -12,7 +12,7 @@
     "* Corresponding reference genome sequence in fasta format (and corresponding index)\n",
     "* Aligned LRTS data in bam format (and corresponding index)\n",
     "\n",
-    "In this tutorial, we provide guidelines about how to prepare aligned LRTS read files (.bam) and the reference genome and annotation data. **Subsequent tutorials on IsoTools workflow do not depend on executing these steps**. We have compiled a small pre-processed demonstration data set, based on a subset of the genome ([download link](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd)). Below, we document how this example data set was produced. \n",
+    "In this tutorial, we provide guidelines about how to prepare aligned LRTS read files (.bam) and the reference genome and annotation data. **Subsequent tutorials on IsoTools workflow do not depend on executing these steps**. We have compiled a small pre-processed demonstration data set, based on a subset of the genome ([download link](https://nc.molgen.mpg.de/cloud/index.php/s/Mf2zMePGBzFWFk8)). Below, we document how this example data set was produced. \n",
     "\n",
     "In order to prepare the files for IsoTools analysis, the following tools are needed:\n",
     "\n",
@@ -369,6 +369,11 @@
     "Please note that when following the PacBio IsoSeq pipeline, resulting sequencing reads are stored in unaligned `bam` files, which need to be formatted in `fastq` before alignment with minimap2. The following command uses the recommended parameters for PacBio isoseq reads (with additional `--MD` for mutation information, which is optional), and sorts the resulting alignment by genomic position. For more details, please refer to the [IsoSeq documentation](https://isoseq.how/)."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "source": "IsoTools supports both PacBio and Oxford Nanopore (ONT) long-read data, including ONT direct RNA sequencing (dRNA). The recommended minimap2 parameters depend on the sequencing protocol:\n\n| Protocol | minimap2 parameters |\n| --- | --- |\n| cDNA_PacBio | `-ax splice:hq -uf` |\n| cDNA_ONT | `-ax splice` |\n| dRNA_ONT | `-ax splice -uf -k14` |\n\nThe command below uses the PacBio Isoseq parameters as an example; substitute the parameters above for ONT cDNA or dRNA data.",
+   "metadata": {}
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -561,4 +566,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}