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Fix example analysis typos.
Correct capitalization of "DNAse" to "DNase" in comments and text, and change 21 bp to 6 bp for variant `47212074_7`. PiperOrigin-RevId: 874697849 Change-Id: I5d1868562b2f1c3fce648ba08964b1a29793a35c
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colabs/example_analysis_workflow.ipynb

Lines changed: 5 additions & 5 deletions
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@@ -895,7 +895,7 @@
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"To make predictions, we'll specify the `interval` (resized to an input sequence\n",
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"length of 2^20 = 1,048,576 bp). We'll also pass in our `requested_outputs`\n",
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"field, which indicates to the model to predict three types of outputs: RNA-seq\n",
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"(a measure of gene expression), DNAse-seq (a measure of DNA accessibility), and\n",
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"(a measure of gene expression), DNase-seq (a measure of DNA accessibility), and\n",
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"ChIP-Histone (a measure of histone modifications, which can indicate active or\n",
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"repressed chromatin states)."
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]
@@ -982,7 +982,7 @@
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" ylabel_template='{biosample_name} ({strand})\\n{name}',\n",
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" filled=True,\n",
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" ),\n",
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" # DNAse tracks.\n",
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" # DNase tracks.\n",
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" plot_components.Tracks(\n",
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" tdata=output.alternate.dnase.filter_to_nonpositive_strand()\n",
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" - output.reference.dnase.filter_to_nonpositive_strand(),\n",
@@ -1000,7 +1000,7 @@
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" annotations=[plot_components.VariantAnnotation([variant])],\n",
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" interval=tal1_interval,\n",
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" title=(\n",
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" 'Effect of variant on predicted RNA Expression, DNAse, and ChIP-Histone'\n",
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" 'Effect of variant on predicted RNA Expression, DNase, and ChIP-Histone'\n",
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" f' in CD34 positive HSC.\\n{variant=}'\n",
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" ),\n",
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")"
@@ -1021,7 +1021,7 @@
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"- RNA-seq coverage is above the horizontal, meaning that *TAL1* is increased\n",
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" in the presence of the alternate sequence relative to the reference\n",
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" sequence.\n",
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"- DNAse-seq indicate changing accessibility near the site of the variant, and\n",
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"- DNase-seq indicate changing accessibility near the site of the variant, and\n",
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" increased accessibility near the transcription start site of *TAL1*.\n",
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"- An increase in H3K27ac and H3K4me1 centered directly on the variant's\n",
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" location, which mark active enhancers.\n",
@@ -1174,7 +1174,7 @@
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"\n",
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"facet_title_by_group = {\n",
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" '47212072_22': 'chr1:47212072\\n21 bp ins.',\n",
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" '47212074_7': 'chr1:47212072\\n21 bp ins.',\n",
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" '47212074_7': 'chr1:47212072\\n6 bp ins.',\n",
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" '47230639_1': 'chr1:47230639\\nSNV',\n",
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" 'MUTE_2': 'chr1:47239296\\n1 bp ins.',\n",
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" 'MUTE_3': 'chr1:47239296\\n2 bp ins.',\n",

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