Recent changes to example

example modified by Jin

Jin — Thu, 28 May 2015 16:06:07 -0000

--- v12
+++ v13
@@ -63,4 +63,19 @@
 =============

 **summary.tsv**
-1  EIF3K   CYP39A1 N   1   Inter_Chromosomal   68  185 18  15  0   0   EIF3K>>CYP39A1(Inter_Chromosomal Canonical 2);EIF3K>>CYP39A1(Inter_Chromosomal Canonical 14);EIF3K>>CYP39A1(Inter_Chromosomal Canonical 163);EIF3K>>CYP39A1(Inter_Chromosomal 6);
+A line says, the first fusion called is EIF3K>>CYP39A1. It is not reciprocal. It is first Tier (Refer to our publication) inter-chromosomal event. It has 68, 185, 18, and 15 encompassing RNA reads, spanning RNA reads, encompassing WGS reads, and spanning WGS reads respectively. It has no reads from the normal WGS data. Then it lists number of reads supporting different fusion transcripts. There is one transcript with 163 reads. 
+
+**reads.txt**
+OK, looking at the summary, this fusion is very striking with large number of supporting reads. You want to look at the supporting reads.
+
+Reads are listed in different categories: Encompassing RNA, Spanning RNA, Encompassing DNA, Spanning DNA ... BLAT them and convince you that this is a good candidate and what functions may this fusion has.
+
+**exons.txt**
+Now there is reason to validate the fusion. exons.tsv contains the target regions to design sequencing probes or PCR primers. 
+
+**breakpoints.tsv**
+Well, it is real and maybe important. Now convey the discovery. This file contains the exact coordinates of fusion junctions and genomic breakpoints. You can have them in some supplementary tables. There are also a bedpe and a vcf file for gene fusions and genomic breakpoints. This could be add to your own pipelines easily. 
+
+
+
+

example modified by Jin

Jin — Thu, 28 May 2015 15:45:04 -0000

--- v11
+++ v12
@@ -62,4 +62,5 @@
 Outputs:
 =============

-
+**summary.tsv**
+1  EIF3K   CYP39A1 N   1   Inter_Chromosomal   68  185 18  15  0   0   EIF3K>>CYP39A1(Inter_Chromosomal Canonical 2);EIF3K>>CYP39A1(Inter_Chromosomal Canonical 14);EIF3K>>CYP39A1(Inter_Chromosomal Canonical 163);EIF3K>>CYP39A1(Inter_Chromosomal 6);

example modified by Jin

Jin — Thu, 28 May 2015 15:43:16 -0000

--- v10
+++ v11
@@ -14,12 +14,12 @@
 Files:
 ======

-reference.fasta             a fasta file containing part of the sequences of chr 6 and 19.
-annot.ucsc.test.txt         a text file with 9 columns, which contains the transcripts information. 
-accepted_hits.bam           sorted bam for mapped tumor rna reads. 
-unmapped.bam                not mapped tumor rna reads.
-dna.tumor.bam               sorted tumor dna bam with soft-clip. 
-dna.normal.bam              sorted normal dna bam with soft-clip. 
+**reference.fasta**             a fasta file containing part of the sequences of chr 6 and 19.
+**annot.ucsc.test.txt**         a text file with 9 columns, which contains the transcripts information. 
+**accepted_hits.bam**           sorted bam for mapped tumor rna reads. 
+**unmapped.bam**                not mapped tumor rna reads.
+**dna.tumor.bam**               sorted tumor dna bam with soft-clip. 
+**dna.normal.bam**              sorted normal dna bam with soft-clip. 

 Note:    (1) All the above files contains only data in the region of 6:46000000-47000000 and  19:39000000-40000000 (unmapped_bam only contains reads relevant to the two genes.
          (2) reference.fasta is 6:1-47000000 and 19:1-40000000)

example modified by Jin

Jin — Thu, 28 May 2015 15:40:58 -0000

--- v9
+++ v10
@@ -14,21 +14,52 @@
 Files:
 ======

-reference.fasta annot.ucsc.test.txt accepted_hits.bam unmapped.bam dna.tumor.bam dna.normal.bam
-a fasta file containing part of the sequences of chr 6 and 19.
-a text file with 9 columns, which contains the transcripts information.
-sorted bam for mapped tumor rna reads. not mapped tumor rna reads.
-sorted tumor dna bam with soft-clip. sorted normal dna bam with soft-clip.
-Note: (1) All the above files contains only data in the region of 6:46000000-47000000 and 19:39000000-40000000 (unmapped_bam only contains reads relevant to the two genes.
-(2) reference.fasta is 6:1-47000000 and 19:1-40000000)
+reference.fasta             a fasta file containing part of the sequences of chr 6 and 19.
+annot.ucsc.test.txt         a text file with 9 columns, which contains the transcripts information. 
+accepted_hits.bam           sorted bam for mapped tumor rna reads. 
+unmapped.bam                not mapped tumor rna reads.
+dna.tumor.bam               sorted tumor dna bam with soft-clip. 
+dna.normal.bam              sorted normal dna bam with soft-clip. 

-Before running the 'fusion' utility to call fusions. A final step of preparing index of reference genome is needed. But only need to do this once. 
+Note:    (1) All the above files contains only data in the region of 6:46000000-47000000 and  19:39000000-40000000 (unmapped_bam only contains reads relevant to the two genes.
+         (2) reference.fasta is 6:1-47000000 and 19:1-40000000)
+

 Preparation:
 ============

-(1) All the bam files (except for unmapped.bam) have been indexed by samtools. (2) Create a folder “bwts”
-mkdir bwts
-Note: this is the folder to store BWTs getting from Integrate. You can use other names rather than “bwts”.
+(1) All the bam files (except for unmapped.bam) have been indexed by samtools. 
+(2) Create a folder “bwts”
+    mkdir bwts
+    Note: this is the folder to store BWTs getting from Integrate. 
+    You can use other names rather than “bwts”.
 (3) Copy executable Integrate to this folder.
 Note: Refer to Reference_Manual_0.1c_5_1_2014.pdf for instructions of compile the executable 
+
+(4) Integrate mkbwt reference.fasta
+
+Call fusion:
+===========
+
+Example command lines:
+ 
+(1) RNA-Seq Tumor + WGS Tumor + WGS Normal
+
+Integrate fusion reference.fasta annot.ucsc.test.txt ./bwts accepted_hits.bam unmapped.bam dna.tumor.bam dna.normal.bam 
+
+(2) RNA-Seq Tumor + WGS Tumor
+
+Integrate fusion reference.fasta annot.ucsc.test.txt ./bwts accepted_hits.bam unmapped.bam dna.tumor.bam 
+   
+(3) RNA-Seq Tumor
+
+Integrate fusion reference.fasta annot.ucsc.test.txt ./bwts accepted_hits.bam unmapped.bam
+
+
+Note: run the commands again using annot.ensembl.test.txt.
+
+
+Outputs:
+=============
+
+

example modified by Jin

Jin — Thu, 28 May 2015 15:35:40 -0000

--- v8
+++ v9
@@ -10,6 +10,7 @@
 The test data contains two small annotation files for two genes of the fusion (annot.ucsc.test.txt and annot.ensembl.test.txt, see Appendix A of Reference_Manual_0.1c_5_1_2014.pdf from Files for how to create annotation files as input). It also contains a tailored reference genome. So everything you need to run the test data is self-contained in the test data.

 you can take a look at the following files:
+
 Files:
 ======

@@ -22,6 +23,7 @@
 (2) reference.fasta is 6:1-47000000 and 19:1-40000000)

 Before running the 'fusion' utility to call fusions. A final step of preparing index of reference genome is needed. But only need to do this once. 
+
 Preparation:
 ============

example modified by Jin

Jin — Thu, 28 May 2015 15:35:25 -0000

--- v7
+++ v8
@@ -12,6 +12,7 @@
 you can take a look at the following files:
 Files:
 ======
+
 reference.fasta annot.ucsc.test.txt accepted_hits.bam unmapped.bam dna.tumor.bam dna.normal.bam
 a fasta file containing part of the sequences of chr 6 and 19.
 a text file with 9 columns, which contains the transcripts information.
@@ -23,6 +24,7 @@
 Before running the 'fusion' utility to call fusions. A final step of preparing index of reference genome is needed. But only need to do this once. 
 Preparation:
 ============
+
 (1) All the bam files (except for unmapped.bam) have been indexed by samtools. (2) Create a folder “bwts”
 mkdir bwts
 Note: this is the folder to store BWTs getting from Integrate. You can use other names rather than “bwts”.

example modified by Jin

Jin — Thu, 28 May 2015 15:35:13 -0000

--- v6
+++ v7
@@ -1,6 +1,5 @@
 Example
--------
--------
+=======

 A test data set with a readme file (Example.pdf) was added to the files for download with v0.1c on May 30th 2014. The input data is still good. However, new versions of the software have changed its outputs. Here let's go through the example again with v0.2.0. 

@@ -12,7 +11,7 @@

 you can take a look at the following files:
 Files:
-------
+======
 reference.fasta annot.ucsc.test.txt accepted_hits.bam unmapped.bam dna.tumor.bam dna.normal.bam
 a fasta file containing part of the sequences of chr 6 and 19.
 a text file with 9 columns, which contains the transcripts information.
@@ -23,7 +22,7 @@

 Before running the 'fusion' utility to call fusions. A final step of preparing index of reference genome is needed. But only need to do this once. 
 Preparation:
-------------
+============
 (1) All the bam files (except for unmapped.bam) have been indexed by samtools. (2) Create a folder “bwts”
 mkdir bwts
 Note: this is the folder to store BWTs getting from Integrate. You can use other names rather than “bwts”.

example modified by Jin

Jin — Thu, 28 May 2015 15:33:40 -0000

--- v5
+++ v6
@@ -1,8 +1,31 @@
 Example
+-------
 -------

 A test data set with a readme file (Example.pdf) was added to the files for download with v0.1c on May 30th 2014. The input data is still good. However, new versions of the software have changed its outputs. Here let's go through the example again with v0.2.0. 

 The test data set is not small, 180Mb in size ofter compression, just to contain one fusion. This is because I want to use the real coordinates of a real fusion. 

-If you want to try INTEGRATE with the test data, you need to download (go to Files) and install (go to [Installation]) first. The test data contains two small annotation files for two genes of the fusion (annot.ucsc.test.txt and annot.ensembl.test.txt, see ).
+If you want to try INTEGRATE with the test data, you need to download (go to Files) and install (go to [Installation]) first. 
+
+The test data contains two small annotation files for two genes of the fusion (annot.ucsc.test.txt and annot.ensembl.test.txt, see Appendix A of Reference_Manual_0.1c_5_1_2014.pdf from Files for how to create annotation files as input). It also contains a tailored reference genome. So everything you need to run the test data is self-contained in the test data. 
+
+you can take a look at the following files:
+Files:
+------
+reference.fasta annot.ucsc.test.txt accepted_hits.bam unmapped.bam dna.tumor.bam dna.normal.bam
+a fasta file containing part of the sequences of chr 6 and 19.
+a text file with 9 columns, which contains the transcripts information.
+sorted bam for mapped tumor rna reads. not mapped tumor rna reads.
+sorted tumor dna bam with soft-clip. sorted normal dna bam with soft-clip.
+Note: (1) All the above files contains only data in the region of 6:46000000-47000000 and 19:39000000-40000000 (unmapped_bam only contains reads relevant to the two genes.
+(2) reference.fasta is 6:1-47000000 and 19:1-40000000)
+
+Before running the 'fusion' utility to call fusions. A final step of preparing index of reference genome is needed. But only need to do this once. 
+Preparation:
+------------
+(1) All the bam files (except for unmapped.bam) have been indexed by samtools. (2) Create a folder “bwts”
+mkdir bwts
+Note: this is the folder to store BWTs getting from Integrate. You can use other names rather than “bwts”.
+(3) Copy executable Integrate to this folder.
+Note: Refer to Reference_Manual_0.1c_5_1_2014.pdf for instructions of compile the executable

example modified by Jin

Jin — Thu, 28 May 2015 15:26:54 -0000

--- v4
+++ v5
@@ -5,4 +5,4 @@

 The test data set is not small, 180Mb in size ofter compression, just to contain one fusion. This is because I want to use the real coordinates of a real fusion. 

-If you want to try INTEGRATE with the test data, you need to [install] 
+If you want to try INTEGRATE with the test data, you need to download (go to Files) and install (go to [Installation]) first. The test data contains two small annotation files for two genes of the fusion (annot.ucsc.test.txt and annot.ensembl.test.txt, see ).

example modified by Jin

Jin — Thu, 28 May 2015 15:23:38 -0000

--- v3
+++ v4
@@ -1,4 +1,8 @@
 Example
 -------

-A test data set with a readme file was added to the files for download 
+A test data set with a readme file (Example.pdf) was added to the files for download with v0.1c on May 30th 2014. The input data is still good. However, new versions of the software have changed its outputs. Here let's go through the example again with v0.2.0. 
+
+The test data set is not small, 180Mb in size ofter compression, just to contain one fusion. This is because I want to use the real coordinates of a real fusion. 
+
+If you want to try INTEGRATE with the test data, you need to [install]