Recent changes to Home

Home modified by Junho Kim

Junho Kim — Mon, 03 Apr 2017 03:31:23 -0000

--- v40
+++ v41
@@ -11,9 +11,9 @@
 [[download_button]]
 


-Update note (Last updated 08-02-2016)
+Update note (Last updated 02-08-2016)
 =======
-###Vecuum-1.0.1 (08-02-2016) *Minor Update###
+###Vecuum-1.0.1 (02-08-2016) *Minor Update###
 #####Improvements:#####
 1. GRCh38 is now supported with '-a' option.
 2. The version of prerequisite softwares is updated. Previous version of SAMtools (0.1.x) can also be used if the path contains version information (e.g. -S /utils/samtools-0.1.19/samtools)

Home modified by Junho Kim

Junho Kim — Mon, 03 Apr 2017 02:16:55 -0000

--- v39
+++ v40
@@ -11,9 +11,9 @@
 [[download_button]]
 


-Update note (Last updated 02-08-2016)
+Update note (Last updated 08-02-2016)
 =======
-###Vecuum-1.0.1 (02-08-2016) *Minor Update###
+###Vecuum-1.0.1 (08-02-2016) *Minor Update###
 #####Improvements:#####
 1. GRCh38 is now supported with '-a' option.
 2. The version of prerequisite softwares is updated. Previous version of SAMtools (0.1.x) can also be used if the path contains version information (e.g. -S /utils/samtools-0.1.19/samtools)

Home modified by Junho Kim

Junho Kim — Tue, 02 Aug 2016 05:46:23 -0000

--- v38
+++ v39
@@ -17,7 +17,7 @@
 #####Improvements:#####
 1. GRCh38 is now supported with '-a' option.
 2. The version of prerequisite softwares is updated. Previous version of SAMtools (0.1.x) can also be used if the path contains version information (e.g. -S /utils/samtools-0.1.19/samtools)
-3. A few minor bugs including output file naming, typos in result files have been fixed.
+3. A few minor bugs including output file naming, presenting transcript ID rather than gene ID, typos in result files have been fixed.
 4. Added "Reccomendation" sections for the first-time users. We highly recommend to use '-A -k' options to analyze entire genome, rather default setttings. A few false variants can be observed regardless of contamination due to the processed pseudogenes.

Home modified by Junho Kim

Junho Kim — Mon, 01 Aug 2016 20:01:51 -0000

--- v37
+++ v38
@@ -102,7 +102,6 @@

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-


 Recommendation
 ======

Home modified by Junho Kim

Junho Kim — Mon, 01 Aug 2016 20:01:06 -0000

--- v36
+++ v37
@@ -102,8 +102,10 @@

 -------------------------------------------
+


-##Recommendation##
+Recommendation
+======
 If you have a list of genes that can be plausible regions of contamination, we recommend to use -R and -k options to reduce the computation times.

     java -jar Vecuum.jar -r <reference_genome.fa> -b <sample_sorted_indexed.bam> -B <bwa_path> -S <samtools_path> -R <tab-delimeted gene="" list="" (chr="" start="" end="" gene_name)=""> -k

Home modified by Junho Kim

Junho Kim — Mon, 01 Aug 2016 19:46:53 -0000

--- v35
+++ v36
@@ -18,7 +18,7 @@
 1. GRCh38 is now supported with '-a' option.
 2. The version of prerequisite softwares is updated. Previous version of SAMtools (0.1.x) can also be used if the path contains version information (e.g. -S /utils/samtools-0.1.19/samtools)
 3. A few minor bugs including output file naming, typos in result files have been fixed.
-4. Added "Reccomendation" sections for the first-time users.
+4. Added "Reccomendation" sections for the first-time users. We highly recommend to use '-A -k' options to analyze entire genome, rather default setttings. A few false variants can be observed regardless of contamination due to the processed pseudogenes.
 


 Prerequisite softwares

Home modified by Junho Kim

Junho Kim — Mon, 01 Aug 2016 19:36:21 -0000

--- v34
+++ v35
@@ -104,7 +104,7 @@
 -------------------------------------------

 ##Recommendation##
-If you have a list of insert genes that can be plausible regions of contamination, we recommend to use -R and -k options to reduce the computation times.
+If you have a list of genes that can be plausible regions of contamination, we recommend to use -R and -k options to reduce the computation times.

     java -jar Vecuum.jar -r <reference_genome.fa> -b <sample_sorted_indexed.bam> -B <bwa_path> -S <samtools_path> -R <tab-delimeted gene="" list="" (chr="" start="" end="" gene_name)=""> -k

Home modified by Junho Kim

Junho Kim — Mon, 01 Aug 2016 19:35:28 -0000

--- v33
+++ v34
@@ -14,7 +14,7 @@
 Update note (Last updated 02-08-2016)
 =======
 ###Vecuum-1.0.1 (02-08-2016) *Minor Update###
-**Changes**
+#####Improvements:#####
 1. GRCh38 is now supported with '-a' option.
 2. The version of prerequisite softwares is updated. Previous version of SAMtools (0.1.x) can also be used if the path contains version information (e.g. -S /utils/samtools-0.1.19/samtools)
 3. A few minor bugs including output file naming, typos in result files have been fixed.

Home modified by Junho Kim

Junho Kim — Mon, 01 Aug 2016 19:34:41 -0000

--- v32
+++ v33
@@ -14,7 +14,7 @@
 Update note (Last updated 02-08-2016)
 =======
 ###Vecuum-1.0.1 (02-08-2016) *Minor Update###
-**Improvements**
+**Changes**
 1. GRCh38 is now supported with '-a' option.
 2. The version of prerequisite softwares is updated. Previous version of SAMtools (0.1.x) can also be used if the path contains version information (e.g. -S /utils/samtools-0.1.19/samtools)
 3. A few minor bugs including output file naming, typos in result files have been fixed.

Home modified by Junho Kim

Junho Kim — Mon, 01 Aug 2016 19:33:52 -0000

--- v31
+++ v32
@@ -14,7 +14,7 @@
 Update note (Last updated 02-08-2016)
 =======
 ###Vecuum-1.0.1 (02-08-2016) *Minor Update###
-#####Improvements#####
+**Improvements**
 1. GRCh38 is now supported with '-a' option.
 2. The version of prerequisite softwares is updated. Previous version of SAMtools (0.1.x) can also be used if the path contains version information (e.g. -S /utils/samtools-0.1.19/samtools)
 3. A few minor bugs including output file naming, typos in result files have been fixed.