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Posted to commits@airavata.apache.org by ma...@apache.org on 2019/06/02 17:22:54 UTC
[airavata-php-gateway] 07/14: update for document and faq page
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 2cdda18ac7490943581b4ecd4b434518ae08faac
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Mon Sep 24 20:04:36 2018 +0000
update for document and faq page
---
public/themes/dreg/partials/doc.blade.php | 76 ++++++++++++++++++++++++++-----
public/themes/dreg/partials/faq.blade.php | 26 ++++++++---
2 files changed, 85 insertions(+), 17 deletions(-)
diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/doc.blade.php
index 9859deb..007ce1b 100755
--- a/public/themes/dreg/partials/doc.blade.php
+++ b/public/themes/dreg/partials/doc.blade.php
@@ -54,20 +54,22 @@ The user can check the status of their 'experiment' by clicking the menu 'Saved
<p class="description" style="padding:16px">
7) <b>Check the results</b><br>
-Once a job is completed, the user can select 'Full results' in the drop-down list and then click <B>'Download'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page, or the user can download any single file from the drop-down list. The downloaded file with the 'tar.gz' extension can be decompressed by the 'tar' command, the file with the 'gz' extension can be decompressed by th [...]
-
-</p>
+Once a job is completed, the user can select 'Full results' in the drop-down list and then LEFT-click <B>'Download'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page, or the user can download any single file from the drop-down list. The downloaded file with the 'tar.gz' extension can be decompressed by the 'tar' command, the file with the 'gz' extension can be decompressed [...]
+</br>
+In <font color="RED">Safari</font>, it could be problematic because Safari tries to unzip the compressed results automatically using a non-compatible compress method. Please check <A href="https://octet.oberlin.edu/does-your-mac-unzip-zip-files-automatically/"> this link </A> to disable this feature.</p>
+
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.summary.png"></img></div>
<p class="description" style="padding:16px">
8) <b>Switch to Genome Browser</b><br>
-The convenient tool ptovided by the gateway is the user can check the results in the Genome Browser by clicking <b>'Switch to genome browser'</B> link. </p>
+The convenient tool provided by the gateway is the user can check the results in the Genome Browser by clicking <b>'Switch to genome browser'</B> link. The genome identifier must be specified by two ways, 1) select from the drop-down list or 2) fill the identifier in the textbox. Please use LEFT-click to open a genome browser window.</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.gbview.png"></img></div>
<p class="description" style="padding:16px">
9) <b>Check the storage</b><br>
-the user can click <b>'Open Folder'</b> link in the experiment summary page to check the storage for the current job or click the menu 'Storage' under the dREG logo to check the folders and files for all jobs(experiments). The following figure shows the data files in the job's folder, including two bigWig files, one result in bedgraph format, two outputs of job scheduler on GPU nodes.</p>
+The user can LEFT-click <b>'Open Folder'</b> link in the experiment summary page to check the storage for the current job or click the menu 'Storage' under the dREG logo to check the folders and files for all jobs(experiments).
+The following figure shows the data files in the job's folder, including two bigWig files, one result in bedgraph format, two outputs of job scheduler on GPU nodes.</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.folder.png"></img></div>
@@ -144,7 +146,7 @@ Airavata PHP Gateway provides an API to build web sites which interact with high
<div class="col-sm-offset-1 col-sm-10 col-xs-12">
<p class="description">
-dREG run generates a compressed file including the dREG and dREG.HD results as follows:
+1) dREG run generates a compressed file including the <font color="green"> dREG results </font> as follows:
</p>
<p class="description"> </p>
@@ -155,23 +157,75 @@ dREG run generates a compressed file including the dREG and dREG.HD results as f
</tr>
<tr>
<td>$PREFIX.dREG.infp.bed.gz</td>
- <td>Informative positions with the scores predicted by the dREG model. <BR>Decompress it with 'gunzip' in Linux.</td>
+ <td>Informative positions with dREG scores predicted by the dREG model. Decompress it with 'gunzip' in Linux.</td>
</tr>
<tr>
<td>$PREFIX.dREG.peak.full.bed.gz</td>
- <td>dREG peaks calling results with score, probability and center position information. <BR>Decompress it with 'gunzip' in Linux.</td>
+ <td>Significant peaks (FDR < 0.05) with dREG scores, p-values and center positions where the maximum dREG scores are located. Decompress it with 'gunzip' in Linux.</td>
</tr>
<tr>
<td>$PREFIX.dREG.peak.score.bed.gz</td>
- <td>dREG peaks calling results only with score. <BR>Decompress it with 'gunzip' in Linux.</td>
+ <td>Significant peaks (FDR < 0.05) only with dREG scores. Decompress it with 'gunzip' in Linux.</td>
+ </tr>
+
+ <tr>
+ <td>$PREFIX.dREG.peak.prob.bed.gz</td>
+ <td>Significant peaks (FDR < 0.05) only with p-values. Decompress it with 'gunzip' in Linux.</td>
</tr>
+
+ <tr>
+ <td>$PREFIX.dREG.raw.peak.bed.gz</td>
+ <td>All raw peaks generated by dREG peak calling, including dREG scores, uncorrected p-values, center positions where the maximum are located in smoothed curves, center positions where the maximim are lcoated in original curve, centroid. Only available in the Web storage.</td>
+ </tr>
+
<tr>
<td>$PREFIX.tar.gz</td>
- <td>Including above 3 files, can be decompressed by 'tar -xvzf' in Linux.</td>
+ <td>Including above 5 files, can be decompressed by 'tar -xvzf' in Linux.</td>
</tr>
</table>
+ <p class="description">
+2) In the Web storage folder there are <font color="green">some files required by the WashU</font> genome browser:
+</p>
+<p class="description"> </p>
+ <table class="table">
+ <tr>
+ <th>File name</th> <th>Description</th> </tr>
+ <tr>
+ <td>$PREFIX.dREG.infp.bw</td>
+ <td>The bigWig file converted from the bed file of informative positions ($PREFIX.dREG.infp.bed.gz).</td>
+ </tr>
+ <tr>
+ <td>$PREFIX.dREG.peak.score.bw</td>
+ <td>The bigWig file converted from the significant peaks (FDR < 0.05) with dREG scores ($PREFIX.dREG.peak.score.bed.gz).</td>
+ </tr>
+ <tr>
+ <td>$PREFIX.dREG.peak.prob.bw</td>
+ <td>The bigWig file converted from the significant peaks (FDR < 0.05) with p-values ($PREFIX.dREG.peak.prob.bed.gz). </td>
+ </tr>
- </div>
+ <tr>
+ <td>*.bed.gz.tbi</td>
+ <td> The index files generated from the corresponding bed files. Please ignore them if you download the results.</td>
+ </tr>
+ </table>
+
+ <p class="description">
+3) There are <font color="green">two log files </font> in the Web storage folder:</p>
+<p class="description"> </p>
+ <table class="table">
+ <tr>
+ <th>File name</th> <th>Description</th> </tr>
+ <tr>
+ <td>$PREFIX.dREG.log</td>
+ <td>Print the summary information after peak calling. If the bigWigs don't meet the requirements of dREG, the warning information will be outputted in this file.
+ </td>
+ </tr>
+ <tr>
+ <td>slurm-??????.out</td>
+ <td>The verbose logging output of dREG package.</td>
+ </tr>
+ </table>
+ </div>
</div>
</div>
diff --git a/public/themes/dreg/partials/faq.blade.php b/public/themes/dreg/partials/faq.blade.php
index fd0bb4e..7550bc9 100755
--- a/public/themes/dreg/partials/faq.blade.php
+++ b/public/themes/dreg/partials/faq.blade.php
@@ -5,25 +5,36 @@
<div class="post-entry">
<p>dREG Gateway is online service that supports Web-based science through the execution of online computational experiments and the management of data. The items below are trying to answer qustions from the users</p>
-<p><b>Q: Which browser works well with the dREG gateway?</b></p>
-<p>A: We have tested in the Firefox and Google Chrome so far. In IE (version 10 or 11) or Safari, WashU geneome browser doesn't work.</p>
-
<p><b>Q: How should I prepare bigWig files for use with the dREG gateway?</b></p>
-<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md#read-mapping"> here </A>.</p>
+<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/proseq2.0"> here </A>.</p>
<p><b>Q: How should I do when I meet the computational failure in the dREG gateway?</b></p>
<p>A: There are two types of error you may have, we explain how to identify your error and how to handle it <A href="https://dreg.dnasequence.org/pages/doc#failure"> here</A>.</p>
+<p><b>Q: Which browser works well with the dREG gateway?</b></p>
+<p>A: We have tested in the Firefox, Google Chrome and Safari so far. For IE (version 10 or 11) and some version of Safari, you maybe have trouble showing sequence data in WashU genome browser. For Safari users, please read next Q&A.</p>
+
+
+<p><b>Q: What should the Safari users be aware of?</b></p>
+<p>A: By default, Safari unzips a zip file automatically when you download it. However dREG results are compressed by the 'bgzip' command which is not compatiable with the Safari method. It would be probelmatic when you download dREG results. Please refer to <A href="https://octet.oberlin.edu/does-your-mac-unzip-zip-files-automatically/"> this link </A> to disable this feature in Safari and then download the compressed results from dREG gateway. </br>
+Secondly, when you click the genome browser link, please use the Left-Click, don't use Right-Click menu and the menu option "open a new tab".
+</p>
+
<p><b>Q: What types of enhancers and promoters can be identified using the dREG gateway?</b></p>
-<p>A: As a general rule of thumb, high-quality datasets provide very similar groups of enhancers and promoters as ChIP-seq for H3K27ac. This suggests that dREG identifies the location of all of the so-called ‘active’ class of enhancers and promoters. </p>
+<p>A: As a general rule of thumb, high-quality datasets provide very similar groups of enhancers and promoters as ChIP-seq for H3K27ac. This suggests that dREG identifies the location of all of the so-called 'active' class of enhancers and promoters. </p>
+
<p><b>Q: Will the dREG gateway work with my data type?</b></p>
<p>A: The dREG gateway will work well with data collected by any run-on and sequencing method, including GRO-seq, PRO-seq, or ChRO-seq. Other methods that map the location of RNA polymerase genome wide using alternative tools (for example, NET-seq) will most likely work well, but are not officially supported.</p>
+
<p><b>Q: Will the pre-trained models work using data from my species?</b></p>
-<p>A: Models are currently available only in mammalian organisms. The length and density of genes, which vary considerably between highly divergent species, affects the way that a transcribed promoter or enhancer looks. For this reason, models can only be used in species . We are working to create models in widely-used model organisms, including drosophila and C. elegans. </p>
+<p>A: Models are currently available only in mammalian organisms. The length and density of genes, which vary considerably between highly divergent species, affects the way that a transcribed promoter or enhancer looks. For this reason, models can only be used in species. We are working to create models in widely-used model organisms, including drosophila and C. elegans. </p>
+
<p><b>Q: How deeply do I need to sequence PRO-seq libraries?</b></p>
<p>A: Sensitivity is reasonable at ~40 million mapped reads and saturates at ~100 million mapped reads. See our analysis here: <A href="http://www.nature.com/nmeth/journal/v12/n5/fig_tab/nmeth.3329_SF3.html">supplementary figure 3 in dREG paper</A>.</p>
+
<p><b>Q: How long do my data and results keep in the dREG gateway?</b></p>
<p>A: One month.</p>
+
<p><b>Q: How to I cite the dREG gateway?</b></p>
<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/>
<A target="_blank" href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">
@@ -34,10 +45,13 @@
<p><b>Q: Do I have to create account before using this service?</b></p>
<p>A: Yes, this system is supported by an NSF funded supercomputing resource known as <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>, who regularly needs to report bulk usage statistics to NSF. Nevertheless, data that you provide are completely safe.</p>
+
<p><b>Q: How do I know the status of the computational nodes? </b></p>
<p>A: Since we can't update this web site very often, the gateway status is updated <A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md">here</A> on the dREG page based on the notifications of the XSEDE community. </p>
+
<p><b>Q: Who do I thank for the computing power? </b></p>
<p>A: This web-based tool is powered by <A title="SciGaP" href="http://www.scigap.org">SciGaP</A> and <A title="Apache Airavata" href="http://airavata.apache.org/">Apache Airavata</A> and the GPU servers are supported by the <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>.</p>
+
<p><b>Q: I have another question that is not on this FAQ. How can I contact you?</b></p>
<p>A: Yes, please contact us with any questions! Zhong(zw355 at cornell.edu). Charles(cgd24 at cornell.edu).</p>