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index.html
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<html>
<head>
<title>RNA-seq viewer</title>
<script>
const REFERENCE_TRACKS = []
/*
const REFERENCE_DATA_ROOT = "gs://macarthurlab-rnaseq/GTEx_ref_data"
REFERENCE_TRACKS.push(...[
{
name: "Muscle",
description: "100 GTEx muscle samples combined by summing raw coverage values and raw splice-junction-spanning read counts across all 100 samples.",
junctions: `${REFERENCE_DATA_ROOT}/muscle_100_GTEx_samples.SJ.out.tab.bed.gz`,
coverage: `${REFERENCE_DATA_ROOT}/muscle_100_GTEx_samples.bigWig`,
},
{
name: "Blood",
description: "100 GTEx blood samples combined by summing raw coverage values and raw splice-junction-spanning read counts across all 100 samples.",
junctions: `${REFERENCE_DATA_ROOT}/blood_100_GTEx_samples.SJ.out.tab.bed.gz`,
coverage: `${REFERENCE_DATA_ROOT}/blood_100_GTEx_samples.bigWig`,
},
{
name: "Fibroblast",
description: "100 GTEx fibroblast samples combined by summing raw coverage values and raw splice-junction-spanning read counts across all 100 samples.",
junctions: `${REFERENCE_DATA_ROOT}/fibs_100_GTEx_samples.SJ.out.tab.bed.gz`,
coverage: `${REFERENCE_DATA_ROOT}/fibs_100_GTEx_samples.bigWig`,
},
];
*/
const SAMPLE_TRACKS = []
SAMPLE_TRACKS.push(...['sampleA', 'sampleB', 'samples_A_and_B'].map(name => { //, 'sampleC', '2sample', '3sample'
return {
name: name.replace('sampleA', 'sample A').replace('sampleB', 'sample B').replace('sampleC', 'sample C').replace('samples_A_and_B', 'samples A + B').replace('3sample', 'samples A + B + C'),
coverage: `gs://seqr-hail/splice_junction_track_test_cases/${name}.chr15-92835700-93031800.bigWig`,
junctions: `gs://seqr-hail/splice_junction_track_test_cases/${name}.chr15-92835700-93031800.SJ.out.bed.gz`,
}
}))
/*
const SAMPLE_DATA_ROOT = "gs://macarthurlab-rnaseq"
SAMPLE_TRACKS.push(...'1179-1, 1211-1, 1258-1, 126BG_CB_M1, 146BO_JB_M1, 149BP_AB_M1, 153BR_JB_M1, 163BV_JE_M1, 164BW_KC_M1, 167BZ_SP_M1, 204H_AM_M1, 205E_BD_M1, 210DB_BW_M1, 227DJ_JP_M1, 247DT_SH_M1, 250DV_LR_M1, 251DW_SD_M1, 252DX_DC_M1, 253DY_HA_M1, 254DZ_WP_M1, 255EA_GC_M1, 26I_SK_M1, 361AL_CC_M1, 373HQ_BTG_M1, 37L_NA_M1, 41M_MW_M1, 431-1_A_3, 431-2_A_2, 432-3_A_2, 437-2_A_2, 437-3_A_2, 447-3_A_3, 46N_RL_M1, 65T_CR_M1, 81AB_MM_M1, 9C_DH_M1, B09-24-1RNA_UNKNOWN, B09-25-1RNA, B09-40-1M, B10-02-1RNA, B11-11-1M, B11-25-1M, B11-48-1M, B12-21-1M, B12-30RNA, B13-07-1M, B13-07-1RNA, B13-15RNA, B13-52-1M, B14-07RNA, B14-117-1RNA-2, B14-130-1M, B14-48-1RNA, B14-70-1RNA, B14-78-1-U, B15-15_1_1, B15-25_1_2, B15-28_1_1, B16-47_1_2, B16-48_1_1, BB0280_CH_AffF_2, BEG_1025-1_T999_R1, BEG_1078-1_T1071_R1, BEG_1230-1_T1227_R1, BEG_14-4_T65_R1, BEG_1438-1_T1339_R1, BEG_851-1_T840_R1, BEG_887-1_T1240_R1, BEG_916-1_T916_R1, BON_B09-27-1_1, BON_B12-33-2_1, BON_B12-71_2_R1, BON_B12-74-1_1, BON_B12-76-1_2, BON_B13-55_1_2, BON_B14-163-1_2, BON_B14-20_1, BON_B14-51_1_2, BON_B14-60-1_2, BON_B14-71-2_1, BON_B14-75-1_1, BON_B15-118_1, BON_B15-125_1_2, BON_B15-26_1_1, BON_B15-76-2_2, BON_B15-98_1_2, BON_B16-19_1, BON_B16-22_1, BON_B16-50_1_2, BON_B16-53-1_1, BON_B16-57_1_2, BON_B16-75-1_2, BON_B16_30_1_1, BON_B16_80_1_1, BON_B17-23_1_R1, BON_B17-28_1_R1, BON_B18-24_1_R1, BON_B18-25_1_R1, BON_B18-54_1_R1, BON_UC219-1_1, BON_UC473_1, CLA_143BN_BB_2, CLA_179CI_GG_2, CLA_180CJ_DP_2, CLA_214DF_AB_2, CLA_329FK_RR_2, CLA_338FT_DM_2, CLA_388HV_XX_1, CLA_62R_CaM_2, CLA_62R_CaM_3, CLA_79Z_CP_2, HK006_0016_R1, HK010_0026_R1, HK011_0029_R1, HK018_0047_2, HK024_0065_R1, HK028_0073_R1, HK044_0109_R1, HK069-0177_2, HK072-001_2, HK085-001_R1, HK088-001_2, HK101-001_R1, HK106-001_R1, ICCV_458_10CC06258_02, K1157-1-4, LIA_EDW01_1, LIA_MAS02_2, LIA_TIS03_2, MAN_0063_01_02, MAN_0063_01_03, MAN_1001_01_M1_D1, MBEL028_001_3, MBEL028_002_1, MBRU030_2, MCOP008_001_2, MESP014_2, MESP021_001_2, MESP039_2, MGLA003_001_2, MMAD002_001_2, MTEH041_001_2, MUN_FAM1_CTRL_01_R1, MUN_FAM1_CTRL_03_R1, MUN_FAM1_CTRL_04_R1, MUN_FAM2_TOTALMDC1A1_02_R1, MUN_FAM2_TOTALMDC1A1_03_R1, MUN_FAM2_TOTALMDC1A1_04_R1, MUN_FAM2_TOTALMDC1A1_05_R1, MUN_FAM3_PARTIALMDC1A1_02_R1, MUN_FAM3_PARTIALMDC1A1_03_R1, MUN_FAM3_PARTIALMDC1A1_05_R1, MUN_FAM4_ATYPICALMDC1A_01_R3, M_0146-01-H1, NH11-441, NH12-1413, NH12-843_Fibroblasts, NH12-843_MyoD_Day5, OUN_HK018_0047_R1, OUN_HK047_0116_R1, OUN_HK079_001_R1, OUN_HK080_001_R1, OUN_HK081_001_R1, OUN_HK112_001_R1, OUN_HK116_001_R1, OUN_HK124_001_R1, OUN_HK137_001_R1, RGP_248_3, RGP_273_3_R1, RGP_54_3_2, RGP_56_3_3, RGP_7_1_2, RGP_7_2_2, RGP_7_3_2, RGP_7_4_2, RGP_7_5_2, RGP_94_3_2, RGP_94_4_2, RP-1850_MUN_FAM1_CTRL_02_R1_v1_RNA_OnPrem, RP-1850_MUN_FAM3_PARTIALMDC1A1_01_R1_v2_RNA_OnPrem, RP-1850_MUN_FAM4_ATYPICALMDC1A_01_R1_v2_RNA_OnPrem, RP-1850_MUN_FAM4_ATYPICALMDC1A_01_R2_v2_RNA_OnPrem, RP-1850_MUN_FAM5_SIBLINGMDC1A_01_R1_v2_RNA_OnPrem, RP-1850_MUN_FAM5_SIBLINGMDC1A_01_R2_v2_RNA_OnPrem, RP-1850_MUN_FAM5_SIBLINGMDC1A_01_R3_v2_RNA_OnPrem, SRPK3_EM__1, SRPK3_JAP_1, SRPK3_USA_1, SWE_36223_1, SWE_36326_1, T1244, T238, T757, T850, T892, TOP_MAAC031_F_Muscle1, UC223-1RNA, UC305-1M, UC316-1M, UC368-1M, UC393-1M, UC84-1RNA, UWA_FAM7_PT_D16-1243_2, VCGS_DLS_FAM1_1_R1, VCGS_FAM11_32_2, VCGS_FAM12_36_2, VCGS_FAM147_459_2, VCGS_FAM148_462_2, VCGS_FAM149_465_2, VCGS_FAM150_468_2, VCGS_FAM1_1_2, VCGS_FAM22_69_2, VCGS_FAM26_81_2, VCGS_FAM27_84_2, VCGS_FAM29_90_R1, VCGS_FAM2_4_2, VCGS_FAM31_97_2, VCGS_FAM39_123_R1, VCGS_FAM3_7_2, VCGS_FAM41_129_2, VCGS_FAM42_132_2, VCGS_FAM49_153_R1, VCGS_FAM4_13_2, VCGS_FAM52_162_3, VCGS_FAM58_181_R1, VCGS_FAM61_190_R1, VCGS_FAM67_209_R1, VCGS_FAM73_227_2, VCGS_FAM84_260_R1, VIL_17_097, VIL_17_098, VIL_17_099, VIL_17_105, VIL_17_106, VIL_17_107, VIL_17_110, VIL_17_111, VIL_17_120, VIL_17_121, VIL_17_141, VIL_17_150, VIL_17_151, VIL_17_152, VIL_17_163, VIL_17_164, VIL_18_045, VIL_18_046, VIL_18_061, VIL_18_120'
.split(', ')
.map(name => {
return {
name: name,
coverage: `${SAMPLE_DATA_ROOT}/bigWig/${name}.bigWig`,
junctions: `${SAMPLE_DATA_ROOT}/SJ_out_bed_for_igvjs/${name}.SJ.out.bed.gz`,
bam: `${SAMPLE_DATA_ROOT}/star/${name}.Aligned.sortedByCoord.out.bam`,
}
}))
*/
</script>
<script src="igv.js"></script>
<script src="state.js"></script>
<script src="google-utils.js"></script>
<script src="main.js"></script>
<!-- script src="https://raw.githubusercontent.com/Sage/jsurl/master/lib/jsurl.js"></script -->
<script src="https://apis.google.com/js/api.js"></script>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1, user-scalable=no">
<link rel="shortcut icon" href="https://igv.org/web/img/favicon.ico">
<link rel="stylesheet" href="style.css">
</head>
<body>
<div id="container">
<div id="left-bar">
<div>
<div style="font-size:14px; padding-top:10px">Min uniquely mapped reads:</div><input type=text" id="minUniquelyMappedReads" value="0" />
<div style="font-size:14px; padding-top:10px">Min total reads:</div><input type=text" id="minTotalReads" value="1" />
<div style="font-size:14px; padding-top:10px">Max fraction multi-mapped reads:</div><input type=text" id="maxFractionMultiMappedReads" value="1" />
<div style="font-size:14px; padding-top:10px">Min spliced alignment overhang:</div><input type=text" id="minSplicedAlignmentOverhang" value="0" />
<div style="font-size:14px; padding-top:10px">Junction thickness based on:</div>
<select id="thicknessBasedOn" name="thicknessBasedOn">
<option value="numUniqueReads">Num Unique Reads</option>
<option value="numReads">Total Number of Reads</option>
<option value="isAnnotatedJunction">Is Known Junction</option>
</select>
<div style="font-size:14px; padding-top:10px">Junction bounce height based on:</div>
<select id="bounceHeightBasedOn" name="bounceHeightBasedOn">
<option value="random">Random</option>
<option value="distance">Distance</option>
<option value="thickness">Thickness</option>
</select>
<div style="font-size:14px; padding-top:10px">Color by:</div>
<select id="colorBy" name="colorBy">
<option value="strand">Strand</option>
<option value="numUniqueReads">Num Unique Reads</option>
<option value="numReads">Total Number of Reads</option>
<option value="isAnnotatedJunction">Is Known Junction</option>
<option value="motif">Donor/Acceptor Motif</option>
</select>
<br />
<div style="font-size:14px; padding-top:10px"><label><input type="checkbox" id="hideAnnotatedJunctions" /> Hide known junctions</label></div>
<div style="font-size:14px; padding-top:10px"><label><input type="checkbox" id="hideUnannotatedJunctions" /> Hide unknown junctions</label></div>
<div style="font-size:14px; padding-top:10px">Known junction label:</div><input type=text" id="labelIsAnnotatedJunction" value="[A]" />
</div>
<!-- h3>REFERENCE TRACKS:</h3 -->
<div id="reference-tracks"><div data-loader="circle-side"></div></div>
<div>
<h3>SAMPLES: <input id="clear-all-samples-button" type="button" value="Clear All" /></h3>
<div id="samples"><div data-loader="circle-side"></div></div>
</div>
<!-- div style="align-content: center; width:100%" id="local-input-panel">
local file(s) or directory: <br/>
<input type="file" id="local-files" name="files[]" multiple /> <br />
</div -->
</div>
<div id="main-panel">
<div id="igv-div"></div>
</div>
</div>
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-153143382-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-153143382-1');
</script>
</body>
</html>