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Home modified by Virmid

Virmid — Wed, 24 Jul 2013 00:19:21 -0000

--- v26
+++ v27
@@ -255,8 +255,8 @@

 C) Merged reads from all homologs (subsubdirectories).

-*mergedCOE.bam: indexed merged concordant one-end reads
-*mergedDOE.bam: indexed merged discordant one-end reads
+* mergedCOE.bam: indexed merged concordant one-end reads
+* mergedDOE.bam: indexed merged discordant one-end reads

 Visualizing the merged bam file using a view (e.g. IGV) help analyze breakpoing manually.

Home modified by Virmid

Virmid — Wed, 24 Jul 2013 00:18:03 -0000

--- v25
+++ v26
@@ -207,7 +207,7 @@

 For example, "chr5:33481 (chr5:33161-34003) 83.0 44+,0- / 0 / 0+,39-" denotes,

-|breakpoint|breakpoint range|breakpoint score|#FU,#RU- / #OV / #FD+,#RD-|
+|breakpoint|breakpoint range|breakpoint score|#FU+,#RU- / #OV / #FD+,#RD-|
 |---|---|---|---|
 |chr5:33481|(chr5:33161-34003)|83.0|44+,0- / 0 / 0+,39-|

@@ -219,10 +219,10 @@

 and the supporting reads are like below:

-* FU: # of forward reads upstream of the breakpoint.
-* RU: # of reverse reads upstream of the breakpoint.
-* FD: # of forward reads downstream of the breakpoint.
-* RD: # of reverse reads downstream of the breakpoint.
+* FU+: # of forward reads upstream of the breakpoint.
+* RU-: # of reverse reads upstream of the breakpoint.
+* FD+: # of forward reads downstream of the breakpoint.
+* RD-: # of reverse reads downstream of the breakpoint.
 * OV: # of mixed set of forward/reverse reads around the breakpoint (25 bp range)

 Because #RU and #FD reads are the counter evidence of the breakpoint, filtering out where #RU!=0 or #FD!=0 increases breakpoint specificity (while possible losing sensitivity). However, the read specificity is fundamentally important, so you should always check the breakpoint score first (see Article).

Home modified by Virmid

Virmid — Wed, 24 Jul 2013 00:15:19 -0000

--- v24
+++ v25
@@ -241,17 +241,17 @@

 A) Reference sequence of the given region (and its flanking regions):

-*chrom_start_end.fa
-*chrom_start_end.left.fa
-*chrom_start_end.right.fa
+* chrom_start_end.fa
+* chrom_start_end.left.fa
+* chrom_start_end.right.fa

 B) It has subsubdirectories each of which corresponds to the homolog of given region.
 Under a subsubdirectory, we have a few bam files.

-*COE.bam: indexed concordant one-end reads mapped to the homolog
-*DOE.bam: indexed discordant one-end reads mapped to the homolog
-*TE.bam: indexed two-end reads mapped to the homolog
-*OOE.bam: indexed orphan one-end reads mapped to the homolog
+* COE.bam: indexed concordant one-end reads mapped to the homolog
+* DOE.bam: indexed discordant one-end reads mapped to the homolog
+* TE.bam: indexed two-end reads mapped to the homolog
+* OOE.bam: indexed orphan one-end reads mapped to the homolog

 C) Merged reads from all homologs (subsubdirectories).

@@ -262,7 +262,7 @@

 D) Special orphan one-end reads that are collected from candidate breakpoints.

-*FE.bam: a list of one-end reads, one of whose end is mapped around candidate breakpoints
+* FE.bam: a list of one-end reads, one of whose end is mapped around candidate breakpoints
 but the other end is orphan. We conduct pairwise alignment between the unmapped read and given regions.

 E) Blat searched discordant one-end reads (.psl)

Home modified by Virmid

Virmid — Wed, 24 Jul 2013 00:14:38 -0000

--- v23
+++ v24
@@ -201,7 +201,7 @@

 #### Final outputs:

-A) [regions].txt.breakpoint - a list of breakpoints discovered by RepreverLoc. Each line is formatted as 
+A) **[regions].txt.breakpoint** - a list of breakpoints discovered by RepreverLoc. Each line is formatted as 

     breakpoint  breakpoint range  breakpoint score  #FU+,#RU- / #OV / #FD+,#RD-

@@ -211,11 +211,13 @@
 |---|---|---|---|
 |chr5:33481|(chr5:33161-34003)|83.0|44+,0- / 0 / 0+,39-|

-
-'breakpoint' is the most probable breakpoint in the donor genome.
-'breakpoint range' is the possible range of the breakpoint.
-'breakpoint score' is the value that corresponds to the confidence of the breakpoint. RepreverLoc
-calls breakpoint when the score is bigger than 2 (by default).
+, where
+
+* 'breakpoint' is the most probable breakpoint in the donor genome.
+* 'breakpoint range' is the possible range of the breakpoint.
+* 'breakpoint score' is the value that corresponds to the confidence of the breakpoint. RepreverLoc calls breakpoint when the score is bigger than 2 (by default).
+
+and the supporting reads are like below:

 * FU: # of forward reads upstream of the breakpoint.
 * RU: # of reverse reads upstream of the breakpoint.
@@ -223,48 +225,44 @@
 * RD: # of reverse reads downstream of the breakpoint.
 * OV: # of mixed set of forward/reverse reads around the breakpoint (25 bp range)

-Because #RU and #FD reads are the counter evidence of the breakpoint, filtering out where #RU!=0 or #FD!=0
-increases breakpoint specificity (while possible losing sensitivity). However, the read specificity
-is fundamentally important, so you should always check the breakpoint score first (see Article).
-
-B) reconstructed sequences.
+Because #RU and #FD reads are the counter evidence of the breakpoint, filtering out where #RU!=0 or #FD!=0 increases breakpoint specificity (while possible losing sensitivity). However, the read specificity is fundamentally important, so you should always check the breakpoint score first (see Article).
+
+B) **reconstructed sequences**

 Final sequences including reconstructed donor duplicons can be found in:

-{working directory}/reconstructed/[region_name]/Result_[region_name].fa
+    {working directory}/reconstructed/[region_name]/Result_[region_name].fa

 The final output is fasta format.

 #### Intermediate output

-Under working directory, one subdirectory is generated for each given region.
-The region name is formatted to "chrom_start_end".
-Under the subdirectory, we have the followings:
+Under working directory, one subdirectory is generated for each given region. The region name is formatted to "chrom_start_end". Under the subdirectory, we have the followings:

 A) Reference sequence of the given region (and its flanking regions):

-chrom_start_end.fa
-chrom_start_end.left.fa
-chrom_start_end.right.fa
+*chrom_start_end.fa
+*chrom_start_end.left.fa
+*chrom_start_end.right.fa

 B) It has subsubdirectories each of which corresponds to the homolog of given region.
 Under a subsubdirectory, we have a few bam files.

-COE.bam: indexed concordant one-end reads mapped to the homolog
-DOE.bam: indexed discordant one-end reads mapped to the homolog
-TE.bam: indexed two-end reads mapped to the homolog
-OOE.bam: indexed orphan one-end reads mapped to the homolog
+*COE.bam: indexed concordant one-end reads mapped to the homolog
+*DOE.bam: indexed discordant one-end reads mapped to the homolog
+*TE.bam: indexed two-end reads mapped to the homolog
+*OOE.bam: indexed orphan one-end reads mapped to the homolog

 C) Merged reads from all homologs (subsubdirectories).

-mergedCOE.bam: indexed merged concordant one-end reads
-mergedDOE.bam: indexed merged discordant one-end reads
+*mergedCOE.bam: indexed merged concordant one-end reads
+*mergedDOE.bam: indexed merged discordant one-end reads

 Visualizing the merged bam file using a view (e.g. IGV) help analyze breakpoing manually.

 D) Special orphan one-end reads that are collected from candidate breakpoints.

-FE.bam: a list of one-end reads, one of whose end is mapped around candidate breakpoints
+*FE.bam: a list of one-end reads, one of whose end is mapped around candidate breakpoints
 but the other end is orphan. We conduct pairwise alignment between the unmapped read and given regions.

 E) Blat searched discordant one-end reads (.psl)
@@ -272,8 +270,9 @@
 
 ## Examples

- There are two example data sets are included. 'example1' contains a small (5x50000bp chromosome) genome.
- The 'original.fa' is a universal reference (like hg18) genome. The 'reference.fa' is a conventional reference in which general SNPs are included; this genome is introduced to represent more realistic situation (we get samples from different individuals, not reference person). 'donor.fa' is a donor genome that contains more SNPs, indels and copy number variations. 'example2' contains a much longer genome (5x1Mbp).
+There are two example data sets are included. 'example1' contains a small (5x50000bp chromosome) genome.
+
+The 'original.fa' is a universal reference (like hg18) genome. The 'reference.fa' is a conventional reference in which general SNPs are included; this genome is introduced to represent more realistic situation (we get samples from different individuals, not reference person). 'donor.fa' is a donor genome that contains more SNPs, indels and copy number variations. 'example2' contains a much longer genome (5x1Mbp).

 You can run the example like below:

@@ -281,5 +280,6 @@

 Note that -g option is used to construct gfServer. And -2 was used to indicate .2bit file.

- Discovered breakpoints are saved in "cnv_regions.txt.breakpoint"
- Reconstructed sequences can be found under "reconstructed/[region_name]/Result_[region_name].fa
+Discovered breakpoints are saved in "cnv_regions.txt.breakpoint"
+
+Reconstructed sequences can be found under "reconstructed/[region_name]/Result_[region_name].fa

Home modified by Virmid

Virmid — Wed, 24 Jul 2013 00:11:26 -0000

--- v22
+++ v23
@@ -201,14 +201,16 @@

 #### Final outputs:

-A) [regions].txt.breakpoint - a list of breakpoints discovered by RepreverLoc. Each line has the following information
-
-'breakpoint' '(breakpoint range)' 'breakpoint score' #FU+,#RU- / #OV / #FD+,#RD-
-For example:
+A) [regions].txt.breakpoint - a list of breakpoints discovered by RepreverLoc. Each line is formatted as 
+
+    breakpoint  breakpoint range  breakpoint score  #FU+,#RU- / #OV / #FD+,#RD-
+
+For example, "chr5:33481 (chr5:33161-34003) 83.0 44+,0- / 0 / 0+,39-" denotes,
+
 |breakpoint|breakpoint range|breakpoint score|#FU,#RU- / #OV / #FD+,#RD-|
 |---|---|---|---|
-
-chr5:33481 (chr5:33161-34003) 83.0 44+,0- / 0 / 0+,39-
+|chr5:33481|(chr5:33161-34003)|83.0|44+,0- / 0 / 0+,39-|
+

 'breakpoint' is the most probable breakpoint in the donor genome.
 'breakpoint range' is the possible range of the breakpoint.

Home modified by Virmid

Virmid — Wed, 24 Jul 2013 00:07:57 -0000

--- v21
+++ v22
@@ -199,13 +199,15 @@

 There are many intermediate/final output files that can be used for further insepction.

-1) Final outputs:
-
-A. [regions].txt.breakpoint - a list of breakpoints discovered by RepreverLoc. Each line has the following
-information
+#### Final outputs:
+
+A) [regions].txt.breakpoint - a list of breakpoints discovered by RepreverLoc. Each line has the following information

 'breakpoint' '(breakpoint range)' 'breakpoint score' #FU+,#RU- / #OV / #FD+,#RD-
 For example:
+|breakpoint|breakpoint range|breakpoint score|#FU,#RU- / #OV / #FD+,#RD-|
+|---|---|---|---|
+
 chr5:33481 (chr5:33161-34003) 83.0 44+,0- / 0 / 0+,39-

 'breakpoint' is the most probable breakpoint in the donor genome.
@@ -223,7 +225,7 @@
 increases breakpoint specificity (while possible losing sensitivity). However, the read specificity
 is fundamentally important, so you should always check the breakpoint score first (see Article).

-B. reconstructed sequences.
+B) reconstructed sequences.

 Final sequences including reconstructed donor duplicons can be found in:

@@ -231,7 +233,7 @@

 The final output is fasta format.

-2) Intermediate output
+#### Intermediate output

 Under working directory, one subdirectory is generated for each given region.
 The region name is formatted to "chrom_start_end".

Home modified by Virmid

Virmid — Wed, 24 Jul 2013 00:01:27 -0000

--- v20
+++ v21
@@ -266,19 +266,16 @@
 E) Blat searched discordant one-end reads (.psl)

 
-** Examples
+## Examples

  There are two example data sets are included. 'example1' contains a small (5x50000bp chromosome) genome.
- The 'original.fa' is a universal reference (like hg18) genome. The 'reference.fa' is a conventional
- reference in which general SNPs are included; this genome is introduced to represent more realistic situation
- (we get samples from different individuals, not reference person). 'donor.fa' is a donor genome that contains
- more SNPs, indels and copy number variations. 'example2' contains a much longer genome (5x1Mbp).
-
- You can run the example like below:
+ The 'original.fa' is a universal reference (like hg18) genome. The 'reference.fa' is a conventional reference in which general SNPs are included; this genome is introduced to represent more realistic situation (we get samples from different individuals, not reference person). 'donor.fa' is a donor genome that contains more SNPs, indels and copy number variations. 'example2' contains a much longer genome (5x1Mbp).
+
+You can run the example like below:

- >java -jar Reprever.jar -R original.fa -C bwaout_sorted.bam -I cnv_region.txt -g2 original.2bit
-
- Note that -g option is used to construct gfServer. And -2 was used to indicate .2bit file.
+    java -jar Reprever.jar -R original.fa -C bwaout_sorted.bam -I cnv_region.txt -g2 original.2bit
+
+Note that -g option is used to construct gfServer. And -2 was used to indicate .2bit file.

  Discovered breakpoints are saved in "cnv_regions.txt.breakpoint"
  Reconstructed sequences can be found under "reconstructed/[region_name]/Result_[region_name].fa

Home modified by Virmid

Virmid — Wed, 24 Jul 2013 00:00:09 -0000

--- v19
+++ v20
@@ -12,6 +12,7 @@
 [Running Reprever](#running)
 [Options and Parameters](#options)
 [Output Files](#output)
+[Running Examples](#example)

 
 ## Quick synopsis
@@ -212,11 +213,11 @@
 'breakpoint score' is the value that corresponds to the confidence of the breakpoint. RepreverLoc
 calls breakpoint when the score is bigger than 2 (by default).

-#FU: # of forward reads upstream of the breakpoint.
-#RU: # of reverse reads upstream of the breakpoint.
-#FD: # of forward reads downstream of the breakpoint.
-#RD: # of reverse reads downstream of the breakpoint.
-#OV: # of mixed set of forward/reverse reads around the breakpoint (25 bp range)
+* FU: # of forward reads upstream of the breakpoint.
+* RU: # of reverse reads upstream of the breakpoint.
+* FD: # of forward reads downstream of the breakpoint.
+* RD: # of reverse reads downstream of the breakpoint.
+* OV: # of mixed set of forward/reverse reads around the breakpoint (25 bp range)

 Because #RU and #FD reads are the counter evidence of the breakpoint, filtering out where #RU!=0 or #FD!=0
 increases breakpoint specificity (while possible losing sensitivity). However, the read specificity
@@ -236,37 +237,36 @@
 The region name is formatted to "chrom_start_end".
 Under the subdirectory, we have the followings:

-A. Reference sequence of the given region (and its flanking regions):
+A) Reference sequence of the given region (and its flanking regions):

 chrom_start_end.fa
 chrom_start_end.left.fa
 chrom_start_end.right.fa

-B. It has subsubdirectories each of which corresponds to the homolog of given region.
+B) It has subsubdirectories each of which corresponds to the homolog of given region.
 Under a subsubdirectory, we have a few bam files.

-COE.bam : indexed concordant one-end reads mapped to the homolog
-DOE.bam : indexed discordant one-end reads mapped to the homolog
-TE.bam : indexed two-end reads mapped to the homolog
-OOE.bam : indexed orphan one-end reads mapped to the homolog
-
-C. Merged reads from all homologs (subsubdirectories).
-
-mergedCOE.bam : indexed merged concordant one-end reads
-mergedDOE.bam : indexed merged discordant one-end reads
+COE.bam: indexed concordant one-end reads mapped to the homolog
+DOE.bam: indexed discordant one-end reads mapped to the homolog
+TE.bam: indexed two-end reads mapped to the homolog
+OOE.bam: indexed orphan one-end reads mapped to the homolog
+
+C) Merged reads from all homologs (subsubdirectories).
+
+mergedCOE.bam: indexed merged concordant one-end reads
+mergedDOE.bam: indexed merged discordant one-end reads

 Visualizing the merged bam file using a view (e.g. IGV) help analyze breakpoing manually.

-D. Special orphan one-end reads that are collected from candidate breakpoints.
-
-FE.bam : a list of one-end reads, one of whose end is mapped around candidate breakpoints
-but the other end is orphan. We conduct pairwise alignment between the unmapped
-read and given regions.
-
-E. Blat searched discordant one-end reads (.psl)
-
-
- VI. Examples
+D) Special orphan one-end reads that are collected from candidate breakpoints.
+
+FE.bam: a list of one-end reads, one of whose end is mapped around candidate breakpoints
+but the other end is orphan. We conduct pairwise alignment between the unmapped read and given regions.
+
+E) Blat searched discordant one-end reads (.psl)
+
+
+** Examples

  There are two example data sets are included. 'example1' contains a small (5x50000bp chromosome) genome.
  The 'original.fa' is a universal reference (like hg18) genome. The 'reference.fa' is a conventional

Home modified by Virmid

Virmid — Tue, 23 Jul 2013 23:15:25 -0000

--- v18
+++ v19
@@ -10,6 +10,8 @@
 [Requirements](#requirements)
 [Preparing input data](#preparing)
 [Running Reprever](#running)
+[Options and Parameters](#options)
+[Output Files](#output)

 
 ## Quick synopsis
@@ -191,8 +193,8 @@
 |-x| FLOAT| gap open penalty for smith-wateran pairwise alignment.|
 |-y| FLOAT| gap extension penalty for smith-waterman pairwise alignment.|

-
- V. Output Files
+
+## Output Files

 There are many intermediate/final output files that can be used for further insepction.

Home modified by Virmid

Virmid — Tue, 23 Jul 2013 22:43:14 -0000

--- v17
+++ v18
@@ -161,7 +161,7 @@

 #### Input Options:

-|Option|Argument|Description|
+|Option|Value|Description|
 |---|---|---|
 |-g| |flag that indicates you want to set up your own gfServer and gfClient. This is mandatory in current version, and automatically turned on; this saves enourmous amount of time when you blat repeatedly.|
 |-2| FILE | specifies the location of [reference].2bit file. If not used, Reprever assumes that it is in the same reference directory|
@@ -169,26 +169,27 @@

 #### Output Options:

-|Option|Argument|Description|
+|Option|Value|Description|
 |---|---|---|
 |-v || verbose. This will print out everything that is going on in Reprever. Use this if your are a reviewer or a debugger.|
 |-o | PATH| the directory where reconstructed results are saved.|

-3) RepreverLoc parameters:
-
--l INT read length. If this is not specified, Reprever tries to infer it by reading 100,000 reads.
--i INT insert size. If not specified, Reprever tries to infer it by reading 100,000 reads.
--m INT minimum % identity for blat match. This is used in homolog search and finding multiple
-mapping reads.
--s INT value for setting minimum score of blat match (blat's match score). The match score is proportional
-to the length of matched region. The minimum score is calculated by s% of the read length.
--p INT threshold percentile for discordant pair. Default is 1%
--k INT minimum breakpoint score to be valid breakpoint. see the article for more detail.
-
-4) RepreverSeq parameters:
-
--x FLOAT gap open penalty for smith-wateran pairwise alignment.
--y FLOAT gap extension penalty for smith-waterman pairwise alignment.
+#### RepreverLoc parameters:
+
+|Option|Value|Description|
+|---|---|---|
+|-l| INT| read length. If this is not specified, Reprever tries to infer it by reading 100,000 reads.|
+|-i| INT| insert size. If not specified, Reprever tries to infer it by reading 100,000 reads.|
+|-m| INT| minimum % identity for blat match. This is used in homolog search and finding multiple mapping reads.|
+|-s| INT| value for setting minimum score of blat match (blat's match score). The match score is proportional to the length of matched region. The minimum score is calculated by s% of the read length.|
+|-p| INT| threshold percentile for discordant pair. Default is 1% |
+|-k| INT| minimum breakpoint score to be valid breakpoint. see the article for more detail.|
+
+#### RepreverSeq parameters:
+|Option|Value|Description|
+|---|---|---|
+|-x| FLOAT| gap open penalty for smith-wateran pairwise alignment.|
+|-y| FLOAT| gap extension penalty for smith-waterman pairwise alignment.|

  V. Output Files