324 lines
14 KiB
HTML
324 lines
14 KiB
HTML
<html lang="en">
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<head>
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<meta charset="UTF-8" />
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<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.2/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-EVSTQN3/azprG1Anm3QDgpJLIm9Nao0Yz1ztcQTwFspd3yD65VohhpuuCOmLASjC" crossorigin="anonymous">
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<style>
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table.table {
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margin-bottom: 4rem;
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}
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video {
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margin: 0 auto 4rem auto;
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max-width: 800px;
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}
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</style>
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</head>
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<body>
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<section class="d-flex flex-column gap-3" style="min-width:800px;max-width:60%; margin:auto">
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<h1>I-GeneMatcher Readme</h1>
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<p>Please follow the tutorial on how to use the I-GeneMatcher. If your video does not play you can download the video from <a href="https://data.d4science.net/vFbH">here</a>.</p>
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<video controls>
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<source type="video/mp4" src="https://cdn.cloud-dev.d4science.org/i-gene/resources/tutorial.mp4"/>
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</video>
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<div>
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<h3>Table description</h3>
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<p>The following tables describe the meaning of the columns in the various data tables produced as output by the I-GeneMatcher.</p>
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<h5>Pair of two guides importing file from CHOPCHOP</h5>
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<table class="table table-striped">
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<thead>
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<tr>
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<td>Column</td>
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<td>Description</td>
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</tr>
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</thead>
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<tbody class="text-primary">
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<tr>
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<td>Rank</td>
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<td>Rank of guide 1 as reported in CHOPCHOP</td>
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</tr>
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<tr>
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<td>Match rank</td>
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<td>Rank of guide 2 as reported in CHOPCHOP</td>
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</tr>
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<tr>
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<td>Distance</td>
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<td>Precise distance between the guides with the selected configuration</td>
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</tr>
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<tr>
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<td>Target sequence</td>
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<td>Sequence of guide 1</td>
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</tr>
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<tr>
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<td>Genomic location</td>
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<td>Position of guide 1</td>
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</tr>
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<tr>
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<td>Match Genomic location</td>
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<td>Position of guide 2</td>
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</tr>
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<tr>
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<td>Strand</td>
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<td>DNA strand that the guide 1 targets</td>
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</tr>
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<tr>
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<td>Match Strand</td>
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<td>DNA strand that the guide 2 targets</td>
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</tr>
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<tr>
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<td>GC content (%)</td>
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<td>GC content percentage of guide 1</td>
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</tr>
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<tr>
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<td>Match GC content (%)</td>
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<td>GC content percentage of guide 2</td>
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</tr>
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<tr>
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<td>Self-complementarity</td>
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<td>Self-complementarity value of guide 1 as reported in CHOPCHOP</td>
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</tr>
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<tr>
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<td>Match Self-complementarity</td>
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<td>Self-complementarity value of guide 2 as reported in CHOPCHOP</td>
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</tr>
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<tr>
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<td>MM0-3</td>
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<td>Targets containing 0 to 3 mismatches for guide 1</td>
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</tr>
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<tr>
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<td>Match MM0-3</td>
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<td>Targets containing 0 to 3 mismatches for guide 2</td>
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</tr>
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<tr>
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<td>Efficiency</td>
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<td>Efficiency value of guide 1 as reported in CHOPCHOP</td>
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</tr>
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<tr>
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<td>Match Efficiency</td>
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<td>Efficiency value of guide 2 as reported in CHOPCHOP</td>
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</tr>
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</tbody>
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</table>
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<h5>Pair of two guides importing file from Crisprscan</h5>
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<table class="table table-striped">
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<thead>
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<tr>
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<td>Column</td>
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<td>Description</td>
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</tr>
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</thead>
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<tbody class="text-primary">
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<tr>
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<td>Rank</td>
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<td>Rank of guide 1 as reported in crisprscan</td>
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</tr>
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<tr>
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<td>Match rank</td>
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<td>Rank of guide 2 as reported in crisprscan</td>
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</tr>
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<tr>
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<td>Distance</td>
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<td>Precise distance between the guides with the selected configuration</td>
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</tr>
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<tr>
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<td>Name</td>
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<td>Targeted chromosome of guide 1</td>
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</tr>
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<tr>
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<td>Match Name</td>
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<td>Targeted chromosome of guide 2</td>
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</tr>
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<tr>
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<td>Start</td>
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<td>Starting genomic position of guide 1</td>
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</tr>
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<tr>
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<td>Match Start</td>
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<td>Starting genomic position of guide 2</td>
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</tr>
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<tr>
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<td>End</td>
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<td>Ending genomic position of guide 1</td>
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</tr>
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<tr>
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<td>Match End</td>
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<td>Ending genomic position of guide 2</td>
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</tr>
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<tr>
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<td>Strand</td>
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<td>DNA strand that the guide 1 targets</td>
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</tr>
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<tr>
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<td>Match Strand</td>
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<td>DNA strand that the guide 2 targets</td>
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</tr>
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<tr>
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<td>Type</td>
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<td>20 nucleotides following the type of PAM for guide 1</td>
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</tr>
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<tr>
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<td>Match Type</td>
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<td>20 nucleotides following the type of PAM for guide 2</td>
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</tr>
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<tr>
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<td>Seq</td>
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<td>Targeting sequence containing the PAM sequence of guide 1</td>
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</tr>
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<tr>
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<td>Match Seq</td>
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<td>Targeting sequence containing the PAM sequence of guide 2</td>
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</tr>
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<tr>
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<td>Sgrna_seq</td>
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<td>Sequence of guide 1</td>
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</tr>
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<tr>
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<td>Match Sgrna_seq</td>
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<td>Sequence of guide 2</td>
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</tr>
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<tr>
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<td>Promoter</td>
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<td>If selected during the crisprscan research</td>
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</tr>
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<tr>
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<td>Match Promoter</td>
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<td>If selected during the crisprscan research</td>
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</tr>
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</tbody>
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<tfoot>
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<tr>
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<td colspan="10">Remaining values as reported by crisprscan. Prefix "Match" always indicates the corresponding values of guide 2.</td>
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</tr>
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</tfoot>
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</table>
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<h5>Restriction enzyme importing file from CHOPCHOP</h5>
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<table class="table table-striped">
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<thead>
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<tr>
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<td>Column</td>
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<td>Description</td>
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</tr>
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</thead>
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<tbody class="text-primary">
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<tr>
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<td>RE sequence</td>
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<td>Restriction site of the selected restriction enzyme</td>
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</tr>
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<tr>
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<td>RE index</td>
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<td>Position of the restriction site</td>
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</tr>
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<tr>
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<td>RE strand</td>
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<td>5'- 3'</td>
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</tr>
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<tr>
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<td>Distance</td>
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<td>Precise distance from the guide</td>
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</tr>
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<tr>
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<td>Rank</td>
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<td>Rank of the guide as reported in CHOPCHOP</td>
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</tr>
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<tr>
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<td>Target sequence</td>
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<td>Sequence of the guide</td>
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</tr>
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<tr>
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<td>Genomic location</td>
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<td>Position of the guide</td>
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</tr>
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<tr>
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<td>Strand</td>
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<td>DNA strand that the guide targets</td>
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</tr>
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<tr>
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<td>GC content (%)</td>
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<td>GC content percentage of the guide</td>
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</tr>
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<tr>
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<td>Self-complementarity</td>
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<td>Self-complementarity value of the guide as reported in CHOPCHOP</td>
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</tr>
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<tr>
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<td>MM0-3</td>
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<td>Targets containing 0 to 3 mismatches</td>
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</tr>
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<tr>
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<td>Efficiency</td>
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<td>Efficiency value as reported in CHOPCHOP</td>
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</tr>
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</tbody>
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</table>
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<h5>Restriction enzyme importing file from Crisprscan</h5>
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<table class="table table-striped">
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<thead>
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<tr>
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<td>Column</td>
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<td>Description</td>
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</tr>
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</thead>
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<tbody class="text-primary">
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<tr>
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<td>RE sequence</td>
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<td>Restriction site of the selected restriction enzyme</td>
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</tr>
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<tr>
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<td>RE index</td>
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<td>Position of the restriction site</td>
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</tr>
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<tr>
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<td>RE strand</td>
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<td>5' - 3'</td>
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</tr>
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<tr>
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<td>Distance</td>
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<td>Precise distance from the guide</td>
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</tr>
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<tr>
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<td>Rank</td>
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<td>Rank of the guide as reported in crisprscan</td>
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</tr>
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<tr>
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<td>Name</td>
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<td>Targeted chromosome</td>
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</tr>
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<tr>
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<td>Start</td>
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<td>Starting genomic position of the guide</td>
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</tr>
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<tr>
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<td>End</td>
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<td>Ending genomic position of the guide</td>
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</tr>
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<tr>
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<td>Strand</td>
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<td>DNA strand that the guide targets</td>
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</tr>
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<tr>
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<td>Type</td>
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<td>20 nucleotides following the type of PAM</td>
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</tr>
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<tr>
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<td>Seq</td>
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<td>Targeting sequence containing the PAM sequence</td>
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</tr>
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<tr>
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<td>Sgrna_seq</td>
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<td>Sequence of the guide</td>
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</tr>
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<tr>
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<td>Promoter</td>
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<td>If selected during the crisprscan research</td>
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</tr>
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</tbody>
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<tfoot>
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<tr>
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<td colspan="10">Remaining values as reported by crisprscan.</td>
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</tr>
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</tfoot>
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</table>
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</div>
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</section>
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</body>
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</html> |