dfjenkins3 · March 2, 2023 07:09 · Aug 25, 2015 · Aug 25, 2015 · Aug 21, 2015 · Aug 21, 2015
diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -148,4 +148,6 @@ snapshot bam3.BRCA1.png
 
 ## Additional Information
 
-Additional information about IGV batch scripts can be found [here](https://www.broadinstitute.org/igv/batch), and a list of commands that you can use in the batch file are [here](https://www.broadinstitute.org/software/igv/PortCommands).
+Additional information can be found on the [IGV website](https://www.broadinstitute.org/igv/batch)
+
+If you want to modify the screenshot in a way that is not available using the bedToIgv tool, a list of available commands can be found  [here](https://www.broadinstitute.org/software/igv/PortCommands). These commands can be added directly to the IGV batch script.
diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -122,7 +122,7 @@ It is possible to load a saved IGV session, although in the past I have found th
 
 ## Run Batch Script
 
-Run the batch script to start saving the screenshots.
+Once you have the window in the desired form, you can run the batch script.  Under the "Tools" menu select "Run Batch Script..."
 
 ![run batch script](https://i.imgur.com/2bdFvPR.png "Run Batch Script")
 

diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -143,7 +143,7 @@ snapshot bam2.BRCA1.png
 new
 load /path/to/bam3/bam3.bam
 goto chr17:41194312-41279500
-snapshot bam2.BRCA1.png
+snapshot bam3.BRCA1.png
 ```
 
 ## Additional Information

diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -137,7 +137,7 @@ load /path/to/bam1/bam1.bam
 goto chr17:41194312-41279500
 snapshot bam1.BRCA1.png
 new
-load /path/to/bam3/bam2.bam
+load /path/to/bam2/bam2.bam
 goto chr17:41194312-41279500
 snapshot bam2.BRCA1.png
 new

diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -12,7 +12,8 @@ IGV provides functionality that allows a user to create a script to take screens
 5. [Load IGV Session](#load-igv-session)
 6. [Optional: Save IGV Session](#optional-save-igv-session)
 7. [Run Batch Script](#run-batch-script)
-8. [Additional Information](#additional-information)
+8. [Screenshots Across Multiple BAM Files](#screenshots-across-multiple-bam-files)
+9. [Additional Information](#additional-information)
 
 ## Requirements
 
@@ -125,6 +126,26 @@ Run the batch script to start saving the screenshots.
 
 ![run batch script](https://i.imgur.com/2bdFvPR.png "Run Batch Script")
 
+## Screenshots Across Multiple BAM Files
+
+It is also possible to take screenshots across several files by loading them sequentially in the batch file, but `bedToIgv` does not support this. In this case the IGV batch script should be created directly. The following example takes a screenshot of the BRCA1 region across three bam files:
+
+```
+new
+snapshotDirectory /path/to/screenshot/directory
+load /path/to/bam1/bam1.bam
+goto chr17:41194312-41279500
+snapshot bam1.BRCA1.png
+new
+load /path/to/bam3/bam2.bam
+goto chr17:41194312-41279500
+snapshot bam2.BRCA1.png
+new
+load /path/to/bam3/bam3.bam
+goto chr17:41194312-41279500
+snapshot bam2.BRCA1.png
+```
+
 ## Additional Information
 
 Additional information about IGV batch scripts can be found [here](https://www.broadinstitute.org/igv/batch), and a list of commands that you can use in the batch file are [here](https://www.broadinstitute.org/software/igv/PortCommands).
diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -12,6 +12,7 @@ IGV provides functionality that allows a user to create a script to take screens
 5. [Load IGV Session](#load-igv-session)
 6. [Optional: Save IGV Session](#optional-save-igv-session)
 7. [Run Batch Script](#run-batch-script)
+8. [Additional Information](#additional-information)
 
 ## Requirements
 

diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -123,3 +123,7 @@ It is possible to load a saved IGV session, although in the past I have found th
 Run the batch script to start saving the screenshots.
 
 ![run batch script](https://i.imgur.com/2bdFvPR.png "Run Batch Script")
+
+## Additional Information
+
+Additional information about IGV batch scripts can be found [here](https://www.broadinstitute.org/igv/batch), and a list of commands that you can use in the batch file are [here](https://www.broadinstitute.org/software/igv/PortCommands).
diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -89,9 +89,9 @@ Notes:
 __Example__:
 
 ```
-[dfj@helium]~/>bedToIgv -path /users/dfj/igv_screenshots/example -slop 100 -i example.bed > example.batch
+[dfj@helium]~/>bedToIgv -path ./examples -slop 100 -i example.bed > example.batch
 [dfj@helium]~/>cat example.batch
-snapshotDirectory /users/dfj/igv_screenshots/example
+snapshotDirectory ./examples
 goto chr1:25158588-25161609
 snapshot chr1_25158688_25161509_slop100.png
 goto chr1:26489713-26490238

diff --git a/example.batch b/example.batch
@@ -0,0 +1,13 @@
+snapshotDirectory ./examples
+goto chr1:25158588-25161609
+snapshot chr1_25158688_25161509_slop100.png
+goto chr1:26489713-26490238
+snapshot chr1_26489813_26490138_slop100.png
+goto chr1:27935252-27935613
+snapshot chr1_27935352_27935513_slop100.png
+goto chr1:28247700-28248208
+snapshot chr1_28247800_28248108_slop100.png
+goto chr1:31574966-31577431
+snapshot chr1_31575066_31577331_slop100.png
+goto chr1:35101322-35112076
+snapshot chr1_35101422_35111976_slop100.png
diff --git a/example.bed b/example.bed
@@ -0,0 +1,6 @@
+chr1	25158688	25161509
+chr1	26489813	26490138
+chr1	27935352	27935513
+chr1	28247800	28248108
+chr1	31575066	31577331
+chr1	35101422	35111976
diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -70,7 +70,7 @@ Options:
         -clps   Collapse the aligned reads prior to taking a snapshot.
                 Default is to no collapse.
 
-        -name   Use the "name" field (column 4) for each image's filename.
+        -name   Use the "name" field (column 4) for each images filename.
                 Default is to use the "chr:start-pos.ext".
 
         -slop   Number of flanking base pairs on the left & right of the image.

diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -83,7 +83,7 @@ Options:
 Notes:
         (1)  The resulting script is meant to be run from within IGV.
         (2)  Unless you use the -sess option, it is assumed that prior to
-                running the script, you've loaded the proper genome and tracks.
+                running the script, youve loaded the proper genome and tracks.
 ```
 
 __Example__:
@@ -108,12 +108,18 @@ snapshot chr1_35101422_35111976_slop100.png
 
 ## Load IGV Session
 
+The IGV batch script is run within IGV. Load the bam, vcf, and BED files that you want to visualize.
+
 ![example session](https://i.imgur.com/aD7swR1.png "Example Session")
 
 ## Optional: Save IGV Session
 
+It is possible to load a saved IGV session, although in the past I have found this to sometimes behave erratically. This is useful if you are interested in creating screenshots from multiple bam files in the same script.
+
 ![save session](https://i.imgur.com/XD9aDAb.png "Save Session")
 
 ## Run Batch Script
 
+Run the batch script to start saving the screenshots.
+
 ![run batch script](https://i.imgur.com/2bdFvPR.png "Run Batch Script")
diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -10,7 +10,8 @@ IGV provides functionality that allows a user to create a script to take screens
 3. [Create BED File](#create-bed-file)
 4. [bedToIgv](#bedtoigv)
 5. [Load IGV Session](#load-igv-session)
-6. [Run Batch Script](#run-batch-script)
+6. [Optional: Save IGV Session](#optional-save-igv-session)
+7. [Run Batch Script](#run-batch-script)
 
 ## Requirements
 
@@ -107,10 +108,12 @@ snapshot chr1_35101422_35111976_slop100.png
 
 ## Load IGV Session
 
-## Run Batch Script
+![example session](https://i.imgur.com/aD7swR1.png "Example Session")
 
-![run batch script](https://i.imgur.com/2bdFvPR.png "Run Batch Script")
+## Optional: Save IGV Session
 
 ![save session](https://i.imgur.com/XD9aDAb.png "Save Session")
 
-![example session](https://i.imgur.com/aD7swR1.png "Example Session")
+## Run Batch Script
+
+![run batch script](https://i.imgur.com/2bdFvPR.png "Run Batch Script")
diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -43,6 +43,8 @@ chr1    35101422    35111976
 
 After creating the BED file, the `bedtools igv` (`bedToIgv`) tool can be used to convert the bed file into an IGV batch script. At a minimum, you should supply a BED file to `bedToIgv`, but you may want to specify an output directory (-path), how to sort the screenshot (-sort), or how much padding to add to the records (-slop).
 
+__Usage__:
+
 ```
 Tool:    bedtools igv (aka bedToIgv)
 Version: v2.21.0

diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -41,7 +41,7 @@ chr1    35101422    35111976
 
 ## bedToIgv
 
-After creating the BED file, the bedtools igv (bedToIgv) tool can be used to convert the bed file into an IGV batch script. At a minimum, you should supply a BED file to bedToIgv, but you may want to specify an output directory (-path), how to sort the screenshot (-sort), or how much padding to add to the records (-slop).
+After creating the BED file, the `bedtools igv` (`bedToIgv`) tool can be used to convert the bed file into an IGV batch script. At a minimum, you should supply a BED file to `bedToIgv`, but you may want to specify an output directory (-path), how to sort the screenshot (-sort), or how much padding to add to the records (-slop).
 
 ```
 Tool:    bedtools igv (aka bedToIgv)

diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -41,6 +41,68 @@ chr1    35101422    35111976
 
 ## bedToIgv
 
+After creating the BED file, the bedtools igv (bedToIgv) tool can be used to convert the bed file into an IGV batch script. At a minimum, you should supply a BED file to bedToIgv, but you may want to specify an output directory (-path), how to sort the screenshot (-sort), or how much padding to add to the records (-slop).
+
+```
+Tool:    bedtools igv (aka bedToIgv)
+Version: v2.21.0
+Summary: Creates a batch script to create IGV images
+         at each interval defined in a BED/GFF/VCF file.
+
+Usage:   bedtools igv [OPTIONS] -i <bed/gff/vcf>
+
+Options:
+        -path   The full path to which the IGV snapshots should be written.
+                (STRING) Default: ./
+
+        -sess   The full path to an existing IGV session file to be
+                loaded prior to taking snapshots.
+
+                (STRING) Default is for no session to be loaded.
+
+        -sort   The type of BAM sorting you would like to apply to each image.
+                Options: base, position, strand, quality, sample, and readGroup
+                Default is to apply no sorting at all.
+
+        -clps   Collapse the aligned reads prior to taking a snapshot.
+                Default is to no collapse.
+
+        -name   Use the "name" field (column 4) for each image's filename.
+                Default is to use the "chr:start-pos.ext".
+
+        -slop   Number of flanking base pairs on the left & right of the image.
+                - (INT) Default = 0.
+
+        -img    The type of image to be created.
+                Options: png, eps, svg
+                Default is png.
+
+Notes:
+        (1)  The resulting script is meant to be run from within IGV.
+        (2)  Unless you use the -sess option, it is assumed that prior to
+                running the script, you've loaded the proper genome and tracks.
+```
+
+__Example__:
+
+```
+[dfj@helium]~/>bedToIgv -path /users/dfj/igv_screenshots/example -slop 100 -i example.bed > example.batch
+[dfj@helium]~/>cat example.batch
+snapshotDirectory /users/dfj/igv_screenshots/example
+goto chr1:25158588-25161609
+snapshot chr1_25158688_25161509_slop100.png
+goto chr1:26489713-26490238
+snapshot chr1_26489813_26490138_slop100.png
+goto chr1:27935252-27935613
+snapshot chr1_27935352_27935513_slop100.png
+goto chr1:28247700-28248208
+snapshot chr1_28247800_28248108_slop100.png
+goto chr1:31574966-31577431
+snapshot chr1_31575066_31577331_slop100.png
+goto chr1:35101322-35112076
+snapshot chr1_35101422_35111976_slop100.png
+```
+
 ## Load IGV Session
 
 ## Run Batch Script

diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -31,7 +31,12 @@ The easiest way to define the regions of interest is to create a [BED](https://g
 __Example__:
 
 ```
-bed
+chr1    25158688    25161509
+chr1    26489813    26490138
+chr1    27935352    27935513
+chr1    28247800    28248108
+chr1    31575066    31577331
+chr1    35101422    35111976
 ```
 
 ## bedToIgv

diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -26,6 +26,14 @@ IGV provides functionality that allows a user to create a script to take screens
 
 ## Create BED File
 
+The easiest way to define the regions of interest is to create a [BED](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) file of the regions. IGV will navigate to the exact coordinates in the bed file. Often you will want to pad the regions for visualization. You can either pad the BED records directly or use the `bedToIgv` script below to pad the records.
+
+__Example__:
+
+```
+bed
+```
+
 ## bedToIgv
 
 ## Load IGV Session

diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -33,3 +33,7 @@ IGV provides functionality that allows a user to create a script to take screens
 ## Run Batch Script
 
 ![run batch script](https://i.imgur.com/2bdFvPR.png "Run Batch Script")
+
+![save session](https://i.imgur.com/XD9aDAb.png "Save Session")
+
+![example session](https://i.imgur.com/aD7swR1.png "Example Session")
diff --git a/IGV_Batch_Screenshots.md b/IGV_Batch_Screenshots.md
@@ -32,3 +32,4 @@ IGV provides functionality that allows a user to create a script to take screens
 
 ## Run Batch Script
 
+![run batch script](https://i.imgur.com/2bdFvPR.png "Run Batch Script")
diff --git a/README.md → IGV_Batch_Screenshots.md b/README.md → IGV_Batch_Screenshots.md
diff --git a/README.md b/README.md
@@ -14,8 +14,8 @@ IGV provides functionality that allows a user to create a script to take screens
 
 ## Requirements
 
-1. [bedtools](www.google.com)
-2. [IGV](www.google.com) version 1.5 or higher
+1. [bedtools](https://github.com/arq5x/bedtools2)
+2. [IGV](https://www.broadinstitute.org/software/igv/download) version 1.5 or higher
 
 ## Workflow
 

diff --git a/README.md b/README.md
@@ -0,0 +1,34 @@
+IGV Batch Screenshots
+=====================
+
+IGV provides functionality that allows a user to create a script to take screenshots of regions of interest.
+
+## Table of Contents
+
+1. [Requirements](#requirements)
+2. [Workflow](#workflow)
+3. [Create BED File](#create-bed-file)
+4. [bedToIgv](#bedtoigv)
+5. [Load IGV Session](#load-igv-session)
+6. [Run Batch Script](#run-batch-script)
+
+## Requirements
+
+1. [bedtools](www.google.com)
+2. [IGV](www.google.com) version 1.5 or higher
+
+## Workflow
+
+1. Create a bed file of regions of interest
+2. Use `bedToIgv` to convert the bed file into an IGV batch script
+3. Open IGV and load the files that you want to visualize
+4. Run the IGV batch script
+
+## Create BED File
+
+## bedToIgv
+
+## Load IGV Session
+
+## Run Batch Script
+
Original file line number	Diff line number	Diff line change
		@@ -32,3 +32,4 @@ IGV provides functionality that allows a user to create a script to take screens

		## Run Batch Script

		![run batch script](https://i.imgur.com/2bdFvPR.png "Run Batch Script")
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