Recent changes to User Manual

User Manual modified by Congting Ye

Congting Ye — Tue, 20 Apr 2021 08:23:57 -0000

--- v17
+++ v18
@@ -216,7 +216,23 @@
 ```
 
  
 ##### \[2] Obtain gene model file of reference genome
-Gene model files of most animal species could be retrieved from [UCSC](http://genome.ucsc.edu/cgi-bin/hgTables?command=start), but for plants they are not available. Currently, we provide gene model files of plants  _Arabidopsis thaliana_ and _Oryza sativa_. We can also help generate the gene model file for other plant species if corresponding genome annotation file was provided.
+Gene model files of most animal species could be retrieved from [UCSC](http://genome.ucsc.edu/cgi-bin/hgTables?command=start), but for plants they are not available. Currently, we provide gene model files of plants  _Arabidopsis thaliana_ and _Oryza sativa_. We can help generate the gene model file for other plant species if corresponding genome annotation file was provided. Users can also generate their own gene model files as follows,
+
+(1) download UCSC tools
+```
+$ wget -c http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred
+$ wget -c http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToBed
+```
+(2) modify Linux file permission
+```
+$ chmod 755 gtfToGenePred genePredToBed
+```
+(3) convert gtf file into bed12
+```
+$ gtfToGenePred Homo_sapiens.GRCh38.86.gtf test.genePhred 
+$ genePredToBed test.genePhred hg.genemodel.bed
+$ rm test.genePhred
+```

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User Manual modified by Congting Ye

Congting Ye — Mon, 05 Oct 2020 01:49:26 -0000

--- v16
+++ v17
@@ -17,7 +17,9 @@

 ---

-***APAtrap*** is a tool capable of refining annotated 3'UTR and identifying novel 3' UTRs and 3' UTR extensions, and aiming to identify all potential APA (alternative polyadenylation) sites and detect genes with differential APA site usage between conditions by leveraging the resolution of RNA-seq data. This software is an open-source tool that follows specifications on website (<http: licenses="" by-nc-sa="" creativecommons.org="" 3.0="">). If you have any question or comment, please contact with Dr. Congting Ye(<yec@xmu.edu.cn>).
+***APAtrap*** is a tool capable of refining annotated 3'UTR and identifying novel 3' UTRs and 3' UTR extensions, and aiming to identify all potential APA (alternative polyadenylation) sites and detect genes with differential APA site usage between conditions by leveraging the resolution of RNA-seq data. 
+This software is an open-source tool that follows specifications on website (<http: licenses="" by-nc-sa="" creativecommons.org="" 3.0="">). 
+If you have any question or comment, please contact with Dr. Congting Ye(<yec@xmu.edu.cn>).

 [Ye C, Long Y, Ji G, Li Q. Q, Wu X (2018) APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. ***Bioinformatics*** 34(11): 1841–1849.](https://academic.oup.com/bioinformatics/article/34/11/1841/4816794) 

</yec@xmu.edu.cn></http:></yec@xmu.edu.cn></http:>

User Manual modified by Congting Ye

Congting Ye — Mon, 05 Oct 2020 01:41:03 -0000

--- v15
+++ v16
@@ -17,8 +17,7 @@

 ---

-***APAtrap*** is a tool capable of refining annotated 3'UTR and identifying novel 3' UTRs and 3' UTR extensions, and aiming to identify all potential APA (alternative polyadenylation) sites and detect genes with differential APA site usage between conditions by leveraging the resolution of RNA-seq data.
-If you have any question or comment, please contact with Dr. Congting Ye(<yec@xmu.edu.cn>).
+***APAtrap*** is a tool capable of refining annotated 3'UTR and identifying novel 3' UTRs and 3' UTR extensions, and aiming to identify all potential APA (alternative polyadenylation) sites and detect genes with differential APA site usage between conditions by leveraging the resolution of RNA-seq data. This software is an open-source tool that follows specifications on website (<http: licenses="" by-nc-sa="" creativecommons.org="" 3.0="">). If you have any question or comment, please contact with Dr. Congting Ye(<yec@xmu.edu.cn>).

 [Ye C, Long Y, Ji G, Li Q. Q, Wu X (2018) APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. ***Bioinformatics*** 34(11): 1841–1849.](https://academic.oup.com/bioinformatics/article/34/11/1841/4816794) 

</yec@xmu.edu.cn></http:></yec@xmu.edu.cn>

User Manual modified by Congting Ye

Congting Ye — Tue, 07 Jul 2020 01:19:19 -0000

--- v14
+++ v15
@@ -244,7 +244,7 @@
 |Gene | Gene ID |      
 |Mean_Squared_Error | Mean squared error of fitting|     
 |Predicted_APA | Coordinates of proximal APA sites inferred by APAtrap (seperated by comma)|
-|Loci | Range of the 3'UTR |
+|Loci | Range of the 3'UTR, of which the terminal site represents the most distal poly(A) site|
 |Group_m_n_Separate_Exp | Expression level of each APA sites (from the most proximal site to the distal site, seperated by comma).  **m,n** indicate the **m**_th sample, **n**_th replicate|
 |Group_m_n_Total_Exp | Total expression level of sample **m**, replicate **n**|

@@ -254,8 +254,8 @@
 |Column Name | Explanation |
 |:---------- |:----------| 
 |p.value | p value|       
-|perc_diff | PD index|
-|r | Pearson product moment correlation coefficient|
+|perc_diff | PD index, percentage difference of APA site usages between two commpared groups, ∈[0,1]|
+|r | Pearson product moment correlation coefficient, ∈[-1,1], a positive value represents that group2 uses more distal poly(A) site (or long 3' UTR) compared to group1, a negtive value represents that group2 uses more proximal poly(A) site (or short 3' UTR) compared to group1 |
 |p.adjust | Adjusted p value|

User Manual modified by Congting Ye

Congting Ye — Fri, 27 Dec 2019 09:10:10 -0000

--- v13
+++ v14
@@ -170,15 +170,15 @@

 Steps of using APAtrap to process the Test_Data.zip:

-* **1st step:** type the following command in the Commond Promt of Linux or Windows,
+* **1st step:** type the following command in the Command Prompt of Linux or Windows,
 ```
 $ ./identifyDistal3UTR -i Sample1.bedgraph Sample2.bedgraph -m hg19.genemodel.bed -o test.utr.bed
 ```
-* **2nd step:** type the following command in the Commond Promt of Linux or Windows,
+* **2nd step:** type the following command in the Command Prompt of Linux or Windows,
 ```
 $ ./predictAPA -i Sample1.bedgraph Sample2.bedgraph -g 2 -n 1 1 -u test.utr.bed -o test.APA.txt
 ```
-* **3rd step:** type the following command in the R Commond Promt,
+* **3rd step:** type the following command in the R Command Prompt,
 ```
 > library(deAPA)
 > deAPA('test.APA.txt', 'test.APA.stat.txt', 1, 2, 1, 1, 20)

User Manual modified by Congting Ye

Congting Ye — Tue, 25 Jun 2019 04:23:06 -0000

--- v12
+++ v13
@@ -20,7 +20,7 @@
 ***APAtrap*** is a tool capable of refining annotated 3'UTR and identifying novel 3' UTRs and 3' UTR extensions, and aiming to identify all potential APA (alternative polyadenylation) sites and detect genes with differential APA site usage between conditions by leveraging the resolution of RNA-seq data.
 If you have any question or comment, please contact with Dr. Congting Ye(<yec@xmu.edu.cn>).

-[Ye C, Long Y, Ji G, Li Q. Q, Wu X (2018) APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. Bioinformatics 34(11): 1841–1849.](https://academic.oup.com/bioinformatics/article/34/11/1841/4816794) 
+[Ye C, Long Y, Ji G, Li Q. Q, Wu X (2018) APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. ***Bioinformatics*** 34(11): 1841–1849.](https://academic.oup.com/bioinformatics/article/34/11/1841/4816794) 

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</yec@xmu.edu.cn>

User Manual modified by Congting Ye

Congting Ye — Tue, 25 Jun 2019 04:22:11 -0000

--- v11
+++ v12
@@ -20,6 +20,8 @@
 ***APAtrap*** is a tool capable of refining annotated 3'UTR and identifying novel 3' UTRs and 3' UTR extensions, and aiming to identify all potential APA (alternative polyadenylation) sites and detect genes with differential APA site usage between conditions by leveraging the resolution of RNA-seq data.
 If you have any question or comment, please contact with Dr. Congting Ye(<yec@xmu.edu.cn>).

+[Ye C, Long Y, Ji G, Li Q. Q, Wu X (2018) APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. Bioinformatics 34(11): 1841–1849.](https://academic.oup.com/bioinformatics/article/34/11/1841/4816794) 
+
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</yec@xmu.edu.cn>

User Manual modified by Congting Ye

Congting Ye — Fri, 20 Jul 2018 10:16:53 -0000

--- v10
+++ v11
@@ -99,8 +99,8 @@
 ###### Necessary parameters:
 ```
 -i  short reads mapping result in bedgraph/wig format, can accept single file or multiple files.
--g  number of groups in the input files, e.g. -g 2.
--n  number of files(duplications) in each group, e.g. -n 1 1.
+-g  number of groups (treatments/conditions) of the input files, e.g. -g 2.
+-n  number of files(biological replicates) in each group (treatment/condition), e.g. -n 1 1.
 -u  3'UTR annotation file in bed format.
 -o  information of the predicted APA sites and their usage.
 ```

User Manual modified by Congting Ye

Congting Ye — Mon, 07 May 2018 02:25:44 -0000

--- v9
+++ v10
@@ -179,7 +179,7 @@
 * **3rd step:** type the following command in the R Commond Promt,
 ```
 > library(deAPA)
-> deAPA(test.APA.txt, test.APA.stat.txt, 1, 2, 1, 1, 20)
+> deAPA('test.APA.txt', 'test.APA.stat.txt', 1, 2, 1, 1, 20)
 ```

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User Manual modified by Congting Ye

Congting Ye — Mon, 18 Dec 2017 08:47:24 -0000

--- v8
+++ v9
@@ -28,7 +28,7 @@

 ---

-###### \[1]. Download and unzip our package - 'APAtrap_Linux.zip' or 'APAtrap_Windows.zip'
+###### \[1]. Download and unzip our package - 'APAtrap_Linux.zip' (or 'APAtrap_Windows.zip', 'APAtrap_MacOS.zip')

 After you download and unzip our APAtrap package, you will see a folder named APAtrap, where 2 standalone executables ('identifyDistal3UTR' and 'predictAPA') compressed from Perl programs and and 1 R package ('deAPA_1.0.tar.gz') are located.