Recent changes to DriverScripts

DriverScripts modified by Robert Kofler

Robert Kofler — Mon, 09 May 2016 09:01:56 -0000

--- v8
+++ v9
@@ -45,7 +45,7 @@
 ######################################################################
 ~~~~~

-### run-map.sh 
+## run-map.sh 

 Driver script for automating mapping. Download here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-map.sh/download

@@ -60,7 +60,7 @@
  * parameter3: output directory
 The result is *outputdir/map-pe.sort.bam*

-### run-popte2.sh
+## run-popte2.sh

 Driver script for automated TE identification with PoPoolationTE2 using default parameters;  Download script here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-popte2.sh/download

@@ -77,7 +77,7 @@
  The  results is *outputdir/tes.finalresult.txt*

-### run-map-popte2 
+## run-map-popte2 

 Driver script for automated mapping of reads and TE identification with PoPoolationTE2 using default parameters; Download the script here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-map-popte2.sh/download
@@ -95,7 +95,7 @@
  * parameter4: the minimum count for TE identification
  The  result is *outputdir/tes.finalresult.txt*

-### run-map-subs-popte2.sh
+## run-map-subs-popte2.sh

 Driver script for automated mapping of reads, subsampling of ppileup files and TE identification with PoPoolationTE2 using default parameters. Download the script here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-map-subs-popte2.sh/download

DriverScripts modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 14:44:15 -0000

--- v7
+++ v8
@@ -75,8 +75,10 @@
  * parameter2: the output directory
  * parameter3: the minimum count for TE identification
  The  results is *outputdir/tes.finalresult.txt*
- 
- ### run-map-popte2 
+
+
+### run-map-popte2 
+

 Driver script for automated mapping of reads and TE identification with PoPoolationTE2 using default parameters; Download the script here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-map-popte2.sh/download

DriverScripts modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 12:32:07 -0000

--- v6
+++ v7
@@ -45,7 +45,8 @@
 ######################################################################
 ~~~~~

-### run-map.sh ###
+### run-map.sh 
+
 Driver script for automating mapping. Download here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-map.sh/download

  First update the configuration (see above) and than run the script like in the following example:
@@ -59,12 +60,11 @@
  * parameter3: output directory
 The result is *outputdir/map-pe.sort.bam*

-### run-popte2.sh###
+### run-popte2.sh

 Driver script for automated TE identification with PoPoolationTE2 using default parameters;  Download script here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-popte2.sh/download

- First update the configuration (see above) and than run the script like in the following example:
-
+First update the configuration (see above) and than run the script like in the following example:

 ~~~~~
 zsh run-popte2.sh input.sort.bam outputdir 2
@@ -76,24 +76,38 @@
  * parameter3: the minimum count for TE identification
  The  results is *outputdir/tes.finalresult.txt*

- ### run-map-popte2 ###
- Driver script for automated mapping of reads and TE identification with PoPoolationTE2 using default parameters; Download the script here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-map-popte2.sh/download
+ ### run-map-popte2 
+ 
+Driver script for automated mapping of reads and TE identification with PoPoolationTE2 using default parameters; Download the script here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-map-popte2.sh/download

  First update the configuration (see above) and than run the script like in the following example:
- 
- 
- ~~~~
- zsh run-map-popte2.sh input_1.fastq.gz input_2.fastq.gz outputdir 2
- ~~~~
- 
- 
+
+
+~~~~~
+zsh run-map-popte2.sh input_1.fastq.gz input_2.fastq.gz outputdir 2
+~~~~~
+
  * parameter1: first fastq file (may be zipped)
  * parameter2: second fastq file (may be zipped)
  * parameter3: output directory
  * parameter4: the minimum count for TE identification
  The  result is *outputdir/tes.finalresult.txt*

+### run-map-subs-popte2.sh
+
+Driver script for automated mapping of reads, subsampling of ppileup files and TE identification with PoPoolationTE2 using default parameters. Download the script here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-map-subs-popte2.sh/download
+
+First update the configuration (see above) and than run the script like in the following example:
+
+~~~~~
+zsh run-map-subs-popte2.sh input_1.fastq.gz input_2.fastq.gz outputdir 2 50
+~~~~~

+ * parameter1: first fastq file (may be zipped)
+ * parameter2: second fastq file (may be zipped)
+ * parameter3: output directory
+ * parameter4: the minimum count for TE identification
+ * parameter5: the target coverage for subsampling the ppileup file
+ The  result is *outputdir/tes.finalresult.txt*

-

DriverScripts modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 12:28:15 -0000

--- v5
+++ v6
@@ -65,9 +65,11 @@

  First update the configuration (see above) and than run the script like in the following example:

-~~~~
+
+~~~~~
 zsh run-popte2.sh input.sort.bam outputdir 2
-~~~~
+~~~~~
+

  * parameter1: a sorted bam file containing paired-end reads mapped to a TE-merged-reference
  * parameter2: the output directory

DriverScripts modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 12:18:39 -0000

--- v4
+++ v5
@@ -48,7 +48,7 @@
 ### run-map.sh ###
 Driver script for automating mapping. Download here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-map.sh/download

-First change the configuration and than run like in the example below:
+ First update the configuration (see above) and than run the script like in the following example:

 ~~~~~
 zsh run-map.sh input_1.fastq.gz input_2.fastq.gz outputdir
@@ -57,13 +57,13 @@
  * parameter1: first fastq file (may be zipped)
  * parameter2: second fastq file (may be zipped)
  * parameter3: output directory
-Result is the file *outputdir/map-pe.sort.bam*
+The result is *outputdir/map-pe.sort.bam*

 ### run-popte2.sh###

-Driver script for automated running of PoPoolationTE2 using default parameters;  Download script here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-popte2.sh/download
+Driver script for automated TE identification with PoPoolationTE2 using default parameters;  Download script here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-popte2.sh/download

-First update the configuration file and run like in the example below
+ First update the configuration (see above) and than run the script like in the following example:

 ~~~~
 zsh run-popte2.sh input.sort.bam outputdir 2
@@ -72,9 +72,24 @@
  * parameter1: a sorted bam file containing paired-end reads mapped to a TE-merged-reference
  * parameter2: the output directory
  * parameter3: the minimum count for TE identification
- Results can be found in *outputdir/tes.finalresult.txt*
+ The  results is *outputdir/tes.finalresult.txt*
+ 
+ ### run-map-popte2 ###
+ Driver script for automated mapping of reads and TE identification with PoPoolationTE2 using default parameters; Download the script here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-map-popte2.sh/download
+ 
+ First update the configuration (see above) and than run the script like in the following example:

+ ~~~~
+ zsh run-map-popte2.sh input_1.fastq.gz input_2.fastq.gz outputdir 2
+ ~~~~
+ 
+ 
+ * parameter1: first fastq file (may be zipped)
+ * parameter2: second fastq file (may be zipped)
+ * parameter3: output directory
+ * parameter4: the minimum count for TE identification
+ The  result is *outputdir/tes.finalresult.txt*

DriverScripts modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 12:11:29 -0000

--- v3
+++ v4
@@ -45,5 +45,38 @@
 ######################################################################
 ~~~~~

+### run-map.sh ###
+Driver script for automating mapping. Download here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-map.sh/download
+
+First change the configuration and than run like in the example below:
+
+~~~~~
+zsh run-map.sh input_1.fastq.gz input_2.fastq.gz outputdir
+~~~~~
+
+ * parameter1: first fastq file (may be zipped)
+ * parameter2: second fastq file (may be zipped)
+ * parameter3: output directory
+Result is the file *outputdir/map-pe.sort.bam*
+
+### run-popte2.sh###
+
+Driver script for automated running of PoPoolationTE2 using default parameters;  Download script here https://sourceforge.net/projects/popoolation-te2/files/driver-scripts/run-popte2.sh/download
+
+First update the configuration file and run like in the example below
+
+~~~~
+zsh run-popte2.sh input.sort.bam outputdir 2
+~~~~
+
+ * parameter1: a sorted bam file containing paired-end reads mapped to a TE-merged-reference
+ * parameter2: the output directory
+ * parameter3: the minimum count for TE identification
+ Results can be found in *outputdir/tes.finalresult.txt*
+ 
+ 

+
+
+

DriverScripts modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 11:52:03 -0000

--- v2
+++ v3
@@ -5,7 +5,7 @@
 This is an advanced topic, so it would help if you have read the manual before and completed the [Walkthrough].
 The driver scripts are provided as shell scripts.

-# The driver scripts =
+# The driver scripts

 ## First steps: configuration 
 Before the driver scripts can be used it is necessary to edit them and fill in the common options.

DriverScripts modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 11:49:42 -0000

--- v1
+++ v2
@@ -1,17 +1,17 @@
 [TOC]

-= Introduction=
+# Introduction
 We generated a couple of shell scripts that allow automatizing some workflows with PoPoolationTE2.
 This is an advanced topic, so it would help if you have read the manual before and completed the [Walkthrough].
 The driver scripts are provided as shell scripts. 

-= The driver scripts =
+# The driver scripts =

-== First steps: configuration ==
+## First steps: configuration 
 Before the driver scripts can be used it is necessary to edit them and fill in the common options.
 The user needs to provide the **absolute** path to the bwa, samtools, PoPoolationTE2 (the jar), the TE-merged-reference and the TE-hierarchy. Editing can be done with any text editor (eg TextWrangler, vi, emacs).

-At the beginning of the file you will find the section:
+At the beginning of each driver script you  will find the following section. Please fill in with the correct values:

 ~~~~~
 #!/bin/zsh

DriverScripts modified by Robert Kofler

Robert Kofler — Tue, 26 Apr 2016 11:48:35 -0000

= Introduction=
We generated a couple of shell scripts that allow automatizing some workflows with PoPoolationTE2.
This is an advanced topic, so it would help if you have read the manual before and completed the [Walkthrough].
The driver scripts are provided as shell scripts.

= The driver scripts =

== First steps: configuration ==
Before the driver scripts can be used it is necessary to edit them and fill in the common options.
The user needs to provide the absolute path to the bwa, samtools, PoPoolationTE2 (the jar), the TE-merged-reference and the TE-hierarchy. Editing can be done with any text editor (eg TextWrangler, vi, emacs).

At the beginning of the file you will find the section:

#!/bin/zsh
#######################################################################
################# CONFIGURATION OF SHELL SCRIPT  ######################
################# PLEASE EDIT THE FOLLOWING      ######################

# Note path to samtools and bwa have to be provided; This makes the analysis
# more reproducible
# path to samtools
samtools="/Volumes/Temp/Robert/programs/samtools-1.2/samtools"

# path to bwa
bwa="/Volumes/Temp/Robert/programs/bwa-0.7.4/bwa"

# threads for bwa
threads=8

# path to the PoPoolationTE2.jar; replace the example with the correct value
popte2="/Volumes/Temp/Robert/programs/popte2/popte2.jar"

# path to the TE-merged-reference; replace the example with the corret value
refg="/Volumes/Temp2/Robert/pop2simulations/refg/chasis1M/chasis1Mtes.fasta"

# path to the TE-hierarchy; replace the example with the correct value
hier="/Volumes/Temp2/Robert/pop2simulations/resources/tehier-ml100noS4.fasta"

##################### END OF CONFIGURATION PART ######################
##################### DO NOT EDIT FROM HERE ON #######################
######################################################################