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@AngryMaciek
AngryMaciek committed Jan 10, 2024
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37 changes: 19 additions & 18 deletions resources/activities-3ss.html
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Expand Up @@ -43,46 +43,47 @@ <h3>Test run with reduced parameters on a sampled dataset</h3>
<br>
<center>
<div style="width: 60%; text-align: left; border: 2px solid black; background-color: #ffffff; padding: 20px; line-height: 1.5;">
This is a summary report for a MAPP run.
Motif count matrices are located under: <code>../modules/CREATE_SITECOUNT_MATRICES/output</code>,
unless external pre-computer resources were specified for this specific workflow execution.
In such case please refer to the pipeline's configuration file and inspect the paths provided
under the field: <code>MAE_sitecount_matrices</code>.
<br>
<br>
Fitted motif activities as well as calculated activity z-scores and their statistical significance
are stored in a tab-separated formatted (TSV) table.
<br>
Rows of this table denote various sequence motifs in specific sliding windows whereas subsequent columns follow the
structure below:
<br>
<br>
<b>ID</b>&nbsp;:&nbsp;unique ID of a sequence motif in a specific sliding window
<b>ID</b>&nbsp;:&nbsp;unique ID of a sequence motif in a specific analysis window
<br>
<b>activities_{sampleID}</b>&nbsp;:&nbsp;motif activities in distinct RNA-Seq samples
<b>activities_{sampleID}</b>&nbsp;:&nbsp;motif activity in the sampleID sample
<br>
<b>deltas_{sampleID}</b>&nbsp;:&nbsp;standard deviations of motif activities
<b>deltas_{sampleID}</b>&nbsp;:&nbsp;delta of motif activity in the sampleID sample
<br>
<b>zscores_{sampleID}</b>&nbsp;:&nbsp;z-scores of motif activities
<b>zscores_{sampleID}</b>&nbsp;:&nbsp;z-score of motif activity in the sampleID sample
<br>
<b>combined.Zscore</b>&nbsp;:&nbsp;overall z-score for a given motif, combined over all samples
<br>
<b>regions_present_fraction</b>&nbsp;:&nbsp;fraction of sites for which the motif was present in a specific window
<b>regions_present_fraction</b>&nbsp;:&nbsp;fraction of sites for which the motif was present in a specific analysis window
<br>
<b>region</b>&nbsp;:&nbsp;sliding window ID
<b>region</b>&nbsp;:&nbsp;analysis window ID
<br>
<b>motif</b>&nbsp;:&nbsp;short sequence motif
<b>motif</b>&nbsp;:&nbsp;motif name
<br>
<b>standard_zscores_{sampleID}</b>&nbsp;:&nbsp;standardised z-scores of motif activities
<b>standard_zscores_{sampleID}</b>&nbsp;:&nbsp;standardised z-score of motif activity in the sampleID sample
<br>
<b>pval_{sampleID}</b>&nbsp;:&nbsp;standardised p-values of motif activities
<b>pval_{sampleID}</b>&nbsp;:&nbsp;standardised p-value of motif activity in the sampleID sample
<br>
<b>corr_pval_{sampleID}</b>&nbsp;:&nbsp;p-values corrected for multiple hypothesis testing
<br>
<b>combined.standard.Zscore</b>&nbsp;:&nbsp;combined standardised z-scores
<br>
<b>max.abs.standard.Zscore</b>&nbsp;:&nbsp;maximum absolute standardised z-score
<b>max.abs.standard.Zscore</b>&nbsp;:&nbsp;maximum absolute standardised z-score across all samples
<br>
<b>significance-marker</b>&nbsp;:&nbsp;statistical significance marker for this motif in this sliding window
<b>significance-marker</b>&nbsp;:&nbsp;statistical significance marker for this motif in this analysis window
<br>
<br>
Motif count matrices are too storage intensive to provide them as a part of a downloadable MAPP report.
However, you can find them in the following location of your MAPP run: <code>../modules/CREATE_SITECOUNT_MATRICES/output</code>,
unless external pre-computed resources were specified for this specific workflow execution.
In such case, please refer to the pipeline's configuration file and inspect the paths you have provided
under the field: <code>MAE_sitecount_matrices</code>.
<br>
<br>
</div>
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37 changes: 19 additions & 18 deletions resources/activities-5ss.html
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Expand Up @@ -43,46 +43,47 @@ <h3>Test run with reduced parameters on a sampled dataset</h3>
<br>
<center>
<div style="width: 60%; text-align: left; border: 2px solid black; background-color: #ffffff; padding: 20px; line-height: 1.5;">
This is a summary report for a MAPP run.
Motif count matrices are located under: <code>../modules/CREATE_SITECOUNT_MATRICES/output</code>,
unless external pre-computer resources were specified for this specific workflow execution.
In such case please refer to the pipeline's configuration file and inspect the paths provided
under the field: <code>MAE_sitecount_matrices</code>.
<br>
<br>
Fitted motif activities as well as calculated activity z-scores and their statistical significance
are stored in a tab-separated formatted (TSV) table.
<br>
Rows of this table denote various sequence motifs in specific sliding windows whereas subsequent columns follow the
structure below:
<br>
<br>
<b>ID</b>&nbsp;:&nbsp;unique ID of a sequence motif in a specific sliding window
<b>ID</b>&nbsp;:&nbsp;unique ID of a sequence motif in a specific analysis window
<br>
<b>activities_{sampleID}</b>&nbsp;:&nbsp;motif activities in distinct RNA-Seq samples
<b>activities_{sampleID}</b>&nbsp;:&nbsp;motif activity in the sampleID sample
<br>
<b>deltas_{sampleID}</b>&nbsp;:&nbsp;standard deviations of motif activities
<b>deltas_{sampleID}</b>&nbsp;:&nbsp;delta of motif activity in the sampleID sample
<br>
<b>zscores_{sampleID}</b>&nbsp;:&nbsp;z-scores of motif activities
<b>zscores_{sampleID}</b>&nbsp;:&nbsp;z-score of motif activity in the sampleID sample
<br>
<b>combined.Zscore</b>&nbsp;:&nbsp;overall z-score for a given motif, combined over all samples
<br>
<b>regions_present_fraction</b>&nbsp;:&nbsp;fraction of sites for which the motif was present in a specific window
<b>regions_present_fraction</b>&nbsp;:&nbsp;fraction of sites for which the motif was present in a specific analysis window
<br>
<b>region</b>&nbsp;:&nbsp;sliding window ID
<b>region</b>&nbsp;:&nbsp;analysis window ID
<br>
<b>motif</b>&nbsp;:&nbsp;short sequence motif
<b>motif</b>&nbsp;:&nbsp;motif name
<br>
<b>standard_zscores_{sampleID}</b>&nbsp;:&nbsp;standardised z-scores of motif activities
<b>standard_zscores_{sampleID}</b>&nbsp;:&nbsp;standardised z-score of motif activity in the sampleID sample
<br>
<b>pval_{sampleID}</b>&nbsp;:&nbsp;standardised p-values of motif activities
<b>pval_{sampleID}</b>&nbsp;:&nbsp;standardised p-value of motif activity in the sampleID sample
<br>
<b>corr_pval_{sampleID}</b>&nbsp;:&nbsp;p-values corrected for multiple hypothesis testing
<br>
<b>combined.standard.Zscore</b>&nbsp;:&nbsp;combined standardised z-scores
<br>
<b>max.abs.standard.Zscore</b>&nbsp;:&nbsp;maximum absolute standardised z-score
<b>max.abs.standard.Zscore</b>&nbsp;:&nbsp;maximum absolute standardised z-score across all samples
<br>
<b>significance-marker</b>&nbsp;:&nbsp;statistical significance marker for this motif in this sliding window
<b>significance-marker</b>&nbsp;:&nbsp;statistical significance marker for this motif in this analysis window
<br>
<br>
Motif count matrices are too storage intensive to provide them as a part of a downloadable MAPP report.
However, you can find them in the following location of your MAPP run: <code>../modules/CREATE_SITECOUNT_MATRICES/output</code>,
unless external pre-computed resources were specified for this specific workflow execution.
In such case, please refer to the pipeline's configuration file and inspect the paths you have provided
under the field: <code>MAE_sitecount_matrices</code>.
<br>
<br>
</div>
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37 changes: 19 additions & 18 deletions resources/activities-pas.html
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Expand Up @@ -43,46 +43,47 @@ <h3>Test run with reduced parameters on a sampled dataset</h3>
<br>
<center>
<div style="width: 60%; text-align: left; border: 2px solid black; background-color: #ffffff; padding: 20px; line-height: 1.5;">
This is a summary report for a MAPP run.
Motif count matrices are located under: <code>../modules/KAPAC/output</code>,
unless external pre-computer resources were specified for this specific workflow execution.
In such case please refer to the pipeline's configuration file and inspect the paths provided
under the field: <code>KPC_sitecount_matrices</code>.
<br>
<br>
Fitted motif activities as well as calculated activity z-scores and their statistical significance
are stored in a tab-separated formatted (TSV) table.
<br>
Rows of this table denote various sequence motifs in specific sliding windows whereas subsequent columns follow the
structure below:
<br>
<br>
<b>ID</b>&nbsp;:&nbsp;unique ID of a sequence motif in a specific sliding window
<b>ID</b>&nbsp;:&nbsp;unique ID of a sequence motif in a specific analysis window
<br>
<b>activities_{sampleID}</b>&nbsp;:&nbsp;motif activities in distinct RNA-Seq samples
<b>activities_{sampleID}</b>&nbsp;:&nbsp;motif activity in the sampleID sample
<br>
<b>deltas_{sampleID}</b>&nbsp;:&nbsp;standard deviations of motif activities
<b>deltas_{sampleID}</b>&nbsp;:&nbsp;delta of motif activity in the sampleID sample
<br>
<b>zscores_{sampleID}</b>&nbsp;:&nbsp;z-scores of motif activities
<b>zscores_{sampleID}</b>&nbsp;:&nbsp;z-score of motif activity in the sampleID sample
<br>
<b>combined.Zscore</b>&nbsp;:&nbsp;overall z-score for a given motif, combined over all samples
<br>
<b>regions_present_fraction</b>&nbsp;:&nbsp;fraction of sites for which the motif was present in a specific window
<b>regions_present_fraction</b>&nbsp;:&nbsp;fraction of sites for which the motif was present in a specific analysis window
<br>
<b>region</b>&nbsp;:&nbsp;sliding window ID
<b>region</b>&nbsp;:&nbsp;analysis window ID
<br>
<b>motif</b>&nbsp;:&nbsp;short sequence motif
<b>motif</b>&nbsp;:&nbsp;motif name
<br>
<b>standard_zscores_{sampleID}</b>&nbsp;:&nbsp;standardised z-scores of motif activities
<b>standard_zscores_{sampleID}</b>&nbsp;:&nbsp;standardised z-score of motif activity in the sampleID sample
<br>
<b>pval_{sampleID}</b>&nbsp;:&nbsp;standardised p-values of motif activities
<b>pval_{sampleID}</b>&nbsp;:&nbsp;standardised p-value of motif activity in the sampleID sample
<br>
<b>corr_pval_{sampleID}</b>&nbsp;:&nbsp;p-values corrected for multiple hypothesis testing
<br>
<b>combined.standard.Zscore</b>&nbsp;:&nbsp;combined standardised z-scores
<br>
<b>max.abs.standard.Zscore</b>&nbsp;:&nbsp;maximum absolute standardised z-score
<b>max.abs.standard.Zscore</b>&nbsp;:&nbsp;maximum absolute standardised z-score across all samples
<br>
<b>significance-marker</b>&nbsp;:&nbsp;statistical significance marker for this motif in this sliding window
<b>significance-marker</b>&nbsp;:&nbsp;statistical significance marker for this motif in this analysis window
<br>
<br>
Motif count matrices are too storage intensive to provide them as a part of a downloadable MAPP report.
However, you can find them in the following location of your MAPP run: <code>../modules/KAPAC/output</code>,
unless external pre-computed resources were specified for this specific workflow execution.
In such case, please refer to the pipeline's configuration file and inspect the paths you have provided
under the field: <code>KPC_sitecount_matrices</code>.
<br>
<br>
</div>
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10 changes: 8 additions & 2 deletions resources/exon-inclusion.html
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Expand Up @@ -46,10 +46,11 @@ <h3>Test run with reduced parameters on a sampled dataset</h3>
Cassette exon inclusion is represented as a ratio of expression
for transcripts which include a specific exon
to all those transcripts which could have possibly included it.
Numerators and denominators of these ratios are stored separately in a tab-separated format (TSV) table.
Numerators and denominators of these ratios are stored in a tab-separated format (TSV) table
in order to still enable TPM-based filtering
Each row in the expression table represents a single cassette exon. The first column
specifies exon coordinates in a BED format.
Each of the next columns stores aggregated TPM values for
Each of the next columns stores TPM values for
specific RNA-Seq samples. Columns with numerators of the inclusion fraction ratios are
denoted with an "_included" suffix whereas denominators are marked with "_total".
Please see the scheme below:
Expand All @@ -61,6 +62,7 @@ <h3>Test run with reduced parameters on a sampled dataset</h3>
<th style="text-align: center; padding: 5px;"><b></b></th>
<th style="text-align: center; padding: 5px;"><b>Sample1_included</b></th>
<th style="text-align: center; padding: 5px;"><b>Sample2_included</b></th>
<th style="text-align: center; padding: 5px;"><b>...</b></th>
<th style="text-align: center; padding: 5px;"><b>Sample1_total</b></th>
<th style="text-align: center; padding: 5px;"><b>Sample2_total</b></th>
<th style="text-align: center; padding: 5px;"><b>...</b></th>
Expand All @@ -72,6 +74,7 @@ <h3>Test run with reduced parameters on a sampled dataset</h3>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>Exon2</b></td>
Expand All @@ -80,6 +83,7 @@ <h3>Test run with reduced parameters on a sampled dataset</h3>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>Exon3</b></td>
Expand All @@ -88,6 +92,7 @@ <h3>Test run with reduced parameters on a sampled dataset</h3>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>...</b></td>
Expand All @@ -96,6 +101,7 @@ <h3>Test run with reduced parameters on a sampled dataset</h3>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
</table>
</center>
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2 changes: 0 additions & 2 deletions resources/gene-expression.html
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Expand Up @@ -49,8 +49,6 @@ <h3>Test run with reduced parameters on a sampled dataset</h3>
<br>
Expression scores are stored as Transcripts-per-Milion (TPM) values in a tab-separated format (TSV) table.
Transcript expression was aggregated over all transcripts for a specific gene.
Please be aware that the TPM scores should not be used to directly compare gene expression across
distinct RNA-Seq samples.
<br>
<br>
Each row in the expression table represents a single, unique gene. The first column
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18 changes: 8 additions & 10 deletions resources/pas-expression.html
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Expand Up @@ -48,26 +48,24 @@ <h3>Test run with reduced parameters on a sampled dataset</h3>
<br>
<br>
Expression scores are stored as Transcripts-per-Milion (TPM) values in a tab-separated format (TSV) table.
Please be aware that the TPM scores should not be used to directly compare Poly(A) sites expression across
distinct RNA-Seq samples.
<br>
<br>
Each row in the expression table represents a single, unique Poly(A) site.
Each row in the expression table represents a single, unique Poly(A) site (PAS).
The first 10 columns contain the following information:
<br>
<b>chrom</b>&nbsp;:&nbsp;chromosome ID
<b>chrom</b>&nbsp;:&nbsp;PAS chromosome
<br>
<b>start</b>&nbsp;:&nbsp;start coordinate (BED format)
<b>start</b>&nbsp;:&nbsp;PAS start coordinate (BED format)
<br>
<b>end</b>&nbsp;:&nbsp;end coordinate (BED format)
<b>end</b>&nbsp;:&nbsp;PAS end coordinate (BED format)
<br>
<b>pas</b>&nbsp;:&nbsp;Poly(A)-sites' ID (as in the PAS Atlas)
<b>pas</b>&nbsp;:&nbsp;PAS ID (as in the PAS annotation used)
<br>
<b>score</b>&nbsp;:&nbsp;minimal support level for a given Poly(A) site
<b>score</b>&nbsp;:&nbsp;score of the PAS annotation used
<br>
<b>strand</b>&nbsp;:&nbsp;sequence strand
<b>strand</b>&nbsp;:&nbsp;PAS strand
<br>
<b>polyAsite_exon_idx</b>&nbsp;:&nbsp;Poly(A) site's index on a specific terminal exon
<b>polyAsite_exon_idx</b>&nbsp;:&nbsp;PAS index on a specific terminal exon
<br>
<b>nr_polyAsites_on_exon</b>&nbsp;:&nbsp;total number of Poly(A) sites on a specific terminal exon
<br>
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2 changes: 0 additions & 2 deletions resources/transcript-expression.html
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Expand Up @@ -48,8 +48,6 @@ <h3>Test run with reduced parameters on a sampled dataset</h3>
<br>
<br>
Expression scores are stored as Transcripts-per-Milion (TPM) values in a tab-separated format (TSV) table.
Please be aware that the TPM scores should not be used to directly compare transcript expression across
distinct RNA-Seq samples.
<br>
<br>
Each row in the expression table represents a single, unique transcript. The first column
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