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readme.html
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<h1>I-GeneMatcher Readme</h1>
<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>
<video controls>
<source type="video/mp4" src="https://cdn.cloud-dev.d4science.org/i-gene/resources/tutorial.mp4"/>
</video>
<div>
<h3>Table description</h3>
<p>The following tables describe the meaning of the columns in the various data tables produced as output by the I-GeneMatcher.</p>
<h5>Pair of two guides importing file from CHOPCHOP</h5>
<table class="table table-striped">
<thead>
<tr>
<td>Column</td>
<td>Description</td>
</tr>
</thead>
<tbody class="text-primary">
<tr>
<td>Rank</td>
<td>Rank of guide 1 as reported in CHOPCHOP</td>
</tr>
<tr>
<td>Match rank</td>
<td>Rank of guide 2 as reported in CHOPCHOP</td>
</tr>
<tr>
<td>Distance</td>
<td>Precise distance between the guides with the selected configuration</td>
</tr>
<tr>
<td>Target sequence</td>
<td>Sequence of guide 1</td>
</tr>
<tr>
<td>Genomic location</td>
<td>Position of guide 1</td>
</tr>
<tr>
<td>Match Genomic location</td>
<td>Position of guide 2</td>
</tr>
<tr>
<td>Strand</td>
<td>DNA strand that the guide 1 targets</td>
</tr>
<tr>
<td>Match Strand</td>
<td>DNA strand that the guide 2 targets</td>
</tr>
<tr>
<td>GC content (%)</td>
<td>GC content percentage of guide 1</td>
</tr>
<tr>
<td>Match GC content (%)</td>
<td>GC content percentage of guide 2</td>
</tr>
<tr>
<td>Self-complementarity</td>
<td>Self-complementarity value of guide 1 as reported in CHOPCHOP</td>
</tr>
<tr>
<td>Match Self-complementarity</td>
<td>Self-complementarity value of guide 2 as reported in CHOPCHOP</td>
</tr>
<tr>
<td>MM0-3</td>
<td>Targets containing 0 to 3 mismatches for guide 1</td>
</tr>
<tr>
<td>Match MM0-3</td>
<td>Targets containing 0 to 3 mismatches for guide 2</td>
</tr>
<tr>
<td>Efficiency</td>
<td>Efficiency value of guide 1 as reported in CHOPCHOP</td>
</tr>
<tr>
<td>Match Efficiency</td>
<td>Efficiency value of guide 2 as reported in CHOPCHOP</td>
</tr>
</tbody>
</table>
<h5>Pair of two guides importing file from Crisprscan</h5>
<table class="table table-striped">
<thead>
<tr>
<td>Column</td>
<td>Description</td>
</tr>
</thead>
<tbody class="text-primary">
<tr>
<td>Rank</td>
<td>Rank of guide 1 as reported in crisprscan</td>
</tr>
<tr>
<td>Match rank</td>
<td>Rank of guide 2 as reported in crisprscan</td>
</tr>
<tr>
<td>Distance</td>
<td>Precise distance between the guides with the selected configuration</td>
</tr>
<tr>
<td>Name</td>
<td>Targeted chromosome of guide 1</td>
</tr>
<tr>
<td>Match Name</td>
<td>Targeted chromosome of guide 2</td>
</tr>
<tr>
<td>Start</td>
<td>Starting genomic position of guide 1</td>
</tr>
<tr>
<td>Match Start</td>
<td>Starting genomic position of guide 2</td>
</tr>
<tr>
<td>End</td>
<td>Ending genomic position of guide 1</td>
</tr>
<tr>
<td>Match End</td>
<td>Ending genomic position of guide 2</td>
</tr>
<tr>
<td>Strand</td>
<td>DNA strand that the guide 1 targets</td>
</tr>
<tr>
<td>Match Strand</td>
<td>DNA strand that the guide 2 targets</td>
</tr>
<tr>
<td>Type</td>
<td>20 nucleotides following the type of PAM for guide 1</td>
</tr>
<tr>
<td>Match Type</td>
<td>20 nucleotides following the type of PAM for guide 2</td>
</tr>
<tr>
<td>Seq</td>
<td>Targeting sequence containing the PAM sequence of guide 1</td>
</tr>
<tr>
<td>Match Seq</td>
<td>Targeting sequence containing the PAM sequence of guide 2</td>
</tr>
<tr>
<td>Sgrna_seq</td>
<td>Sequence of guide 1</td>
</tr>
<tr>
<td>Match Sgrna_seq</td>
<td>Sequence of guide 2</td>
</tr>
<tr>
<td>Promoter</td>
<td>If selected during the crisprscan research</td>
</tr>
<tr>
<td>Match Promoter</td>
<td>If selected during the crisprscan research</td>
</tr>
</tbody>
<tfoot>
<tr>
<td colspan="10">Remaining values as reported by crisprscan. Prefix "Match" always indicates the corresponding values of guide 2.</td>
</tr>
</tfoot>
</table>
<h5>Restriction enzyme importing file from CHOPCHOP</h5>
<table class="table table-striped">
<thead>
<tr>
<td>Column</td>
<td>Description</td>
</tr>
</thead>
<tbody class="text-primary">
<tr>
<td>RE sequence</td>
<td>Restriction site of the selected restriction enzyme</td>
</tr>
<tr>
<td>RE index</td>
<td>Position of the restriction site</td>
</tr>
<tr>
<td>RE strand</td>
<td>5'- 3'</td>
</tr>
<tr>
<td>Distance</td>
<td>Precise distance from the guide</td>
</tr>
<tr>
<td>Rank</td>
<td>Rank of the guide as reported in CHOPCHOP</td>
</tr>
<tr>
<td>Target sequence</td>
<td>Sequence of the guide</td>
</tr>
<tr>
<td>Genomic location</td>
<td>Position of the guide</td>
</tr>
<tr>
<td>Strand</td>
<td>DNA strand that the guide targets</td>
</tr>
<tr>
<td>GC content (%)</td>
<td>GC content percentage of the guide</td>
</tr>
<tr>
<td>Self-complementarity</td>
<td>Self-complementarity value of the guide as reported in CHOPCHOP</td>
</tr>
<tr>
<td>MM0-3</td>
<td>Targets containing 0 to 3 mismatches</td>
</tr>
<tr>
<td>Efficiency</td>
<td>Efficiency value as reported in CHOPCHOP</td>
</tr>
</tbody>
</table>
<h5>Restriction enzyme importing file from Crisprscan</h5>
<table class="table table-striped">
<thead>
<tr>
<td>Column</td>
<td>Description</td>
</tr>
</thead>
<tbody class="text-primary">
<tr>
<td>RE sequence</td>
<td>Restriction site of the selected restriction enzyme</td>
</tr>
<tr>
<td>RE index</td>
<td>Position of the restriction site</td>
</tr>
<tr>
<td>RE strand</td>
<td>5' - 3'</td>
</tr>
<tr>
<td>Distance</td>
<td>Precise distance from the guide</td>
</tr>
<tr>
<td>Rank</td>
<td>Rank of the guide as reported in crisprscan</td>
</tr>
<tr>
<td>Name</td>
<td>Targeted chromosome</td>
</tr>
<tr>
<td>Start</td>
<td>Starting genomic position of the guide</td>
</tr>
<tr>
<td>End</td>
<td>Ending genomic position of the guide</td>
</tr>
<tr>
<td>Strand</td>
<td>DNA strand that the guide targets</td>
</tr>
<tr>
<td>Type</td>
<td>20 nucleotides following the type of PAM</td>
</tr>
<tr>
<td>Seq</td>
<td>Targeting sequence containing the PAM sequence</td>
</tr>
<tr>
<td>Sgrna_seq</td>
<td>Sequence of the guide</td>
</tr>
<tr>
<td>Promoter</td>
<td>If selected during the crisprscan research</td>
</tr>
</tbody>
<tfoot>
<tr>
<td colspan="10">Remaining values as reported by crisprscan.</td>
</tr>
</tfoot>
</table>
</div>
</section>
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