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895 | 895 | "To make predictions, we'll specify the `interval` (resized to an input sequence\n", |
896 | 896 | "length of 2^20 = 1,048,576 bp). We'll also pass in our `requested_outputs`\n", |
897 | 897 | "field, which indicates to the model to predict three types of outputs: RNA-seq\n", |
898 | | - "(a measure of gene expression), DNAse-seq (a measure of DNA accessibility), and\n", |
| 898 | + "(a measure of gene expression), DNase-seq (a measure of DNA accessibility), and\n", |
899 | 899 | "ChIP-Histone (a measure of histone modifications, which can indicate active or\n", |
900 | 900 | "repressed chromatin states)." |
901 | 901 | ] |
|
982 | 982 | " ylabel_template='{biosample_name} ({strand})\\n{name}',\n", |
983 | 983 | " filled=True,\n", |
984 | 984 | " ),\n", |
985 | | - " # DNAse tracks.\n", |
| 985 | + " # DNase tracks.\n", |
986 | 986 | " plot_components.Tracks(\n", |
987 | 987 | " tdata=output.alternate.dnase.filter_to_nonpositive_strand()\n", |
988 | 988 | " - output.reference.dnase.filter_to_nonpositive_strand(),\n", |
|
1000 | 1000 | " annotations=[plot_components.VariantAnnotation([variant])],\n", |
1001 | 1001 | " interval=tal1_interval,\n", |
1002 | 1002 | " title=(\n", |
1003 | | - " 'Effect of variant on predicted RNA Expression, DNAse, and ChIP-Histone'\n", |
| 1003 | + " 'Effect of variant on predicted RNA Expression, DNase, and ChIP-Histone'\n", |
1004 | 1004 | " f' in CD34 positive HSC.\\n{variant=}'\n", |
1005 | 1005 | " ),\n", |
1006 | 1006 | ")" |
|
1021 | 1021 | "- RNA-seq coverage is above the horizontal, meaning that *TAL1* is increased\n", |
1022 | 1022 | " in the presence of the alternate sequence relative to the reference\n", |
1023 | 1023 | " sequence.\n", |
1024 | | - "- DNAse-seq indicate changing accessibility near the site of the variant, and\n", |
| 1024 | + "- DNase-seq indicate changing accessibility near the site of the variant, and\n", |
1025 | 1025 | " increased accessibility near the transcription start site of *TAL1*.\n", |
1026 | 1026 | "- An increase in H3K27ac and H3K4me1 centered directly on the variant's\n", |
1027 | 1027 | " location, which mark active enhancers.\n", |
|
1174 | 1174 | "\n", |
1175 | 1175 | "facet_title_by_group = {\n", |
1176 | 1176 | " '47212072_22': 'chr1:47212072\\n21 bp ins.',\n", |
1177 | | - " '47212074_7': 'chr1:47212072\\n21 bp ins.',\n", |
| 1177 | + " '47212074_7': 'chr1:47212072\\n6 bp ins.',\n", |
1178 | 1178 | " '47230639_1': 'chr1:47230639\\nSNV',\n", |
1179 | 1179 | " 'MUTE_2': 'chr1:47239296\\n1 bp ins.',\n", |
1180 | 1180 | " 'MUTE_3': 'chr1:47239296\\n2 bp ins.',\n", |
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