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Home modified by Sora Kim

Sora Kim — Tue, 24 Jan 2017 04:04:51 -0000

--- v9
+++ v10
@@ -38,17 +38,17 @@
  
 ### Required arguments 
 ~~~~
-    -r, --ref     FILE  reference file
     -1, --read1   FILE  RNA sequencing read1 file
-    -r, --ref     FILE  reference file path
-    -m, --marker  INT   marker information file
+    -r, --ref     PATH  reference file path
+    -m, --marker  FILE  marker information file
 ~~~~
  
 ### Optional arguments

 ~~~~
     -2, --read2         FILE  RNA sequencing read2 file
-    -d, --outDir        DIR   output directory
+    -o, --outDir        DIR   output directory
+    -l, --prim          INT   primer length default=15
 ~~~~

Home modified by Sora Kim

Sora Kim — Tue, 24 Jan 2017 04:02:56 -0000

--- v8
+++ v9
@@ -38,10 +38,10 @@
  
 ### Required arguments 
 ~~~~
-    -r, --ref   FILE  reference file
-    -1, --read1 FILE  RNA sequencing read1 file
-    -v, --vcf   FILE  VCF formatted mutation file
-    -n, --nmer  INT   predicted size of neoantigen
+    -r, --ref     FILE  reference file
+    -1, --read1   FILE  RNA sequencing read1 file
+    -r, --ref     FILE  reference file path
+    -m, --marker  INT   marker information file
 ~~~~
  
 ### Optional arguments

Home modified by Sora Kim

Sora Kim — Tue, 24 Jan 2017 02:27:01 -0000

--- v7
+++ v8
@@ -26,7 +26,7 @@

 ## Usage for Windows
-#### **Right click on the image and select "Open Image in New Tab"** ####
+###### **Right click on the image and select "Open Image in New Tab"** ######
 [[img src=STRoNGS_guide.png alt=STRoNGSv1.0]]

Home modified by Sora Kim

Sora Kim — Tue, 24 Jan 2017 02:26:40 -0000

--- v6
+++ v7
@@ -26,7 +26,7 @@

 ## Usage for Windows
-###**Right click on the image and select "Open Image in New Tab"**###
+#### **Right click on the image and select "Open Image in New Tab"** ####
 [[img src=STRoNGS_guide.png alt=STRoNGSv1.0]]

Home modified by Sora Kim

Sora Kim — Tue, 24 Jan 2017 02:26:09 -0000

--- v5
+++ v6
@@ -26,7 +26,7 @@

 ## Usage for Windows
-**Right click on the image and select "Open Image in New Tab"**
+###**Right click on the image and select "Open Image in New Tab"**###
 [[img src=STRoNGS_guide.png alt=STRoNGSv1.0]]

Home modified by Sora Kim

Sora Kim — Tue, 24 Jan 2017 02:24:27 -0000

--- v4
+++ v5
@@ -26,6 +26,7 @@

 ## Usage for Windows
+**Right click on the image and select "Open Image in New Tab"**
 [[img src=STRoNGS_guide.png alt=STRoNGSv1.0]]

Home modified by Sora Kim

Sora Kim — Tue, 24 Jan 2017 02:14:34 -0000

--- v3
+++ v4
@@ -53,7 +53,7 @@

 ### Input
-* STRoNGS requires raw FASTQ file format as input. It can be use a single or paired files.
+* STRoNGS requires raw FASTQ file or compressed form of FASTQ.GZ as input format. It can be use a single or paired files.

Home modified by Sora Kim

Sora Kim — Tue, 24 Jan 2017 02:13:38 -0000

--- v2
+++ v3
@@ -53,43 +53,24 @@

 ### Input
-* Reference file (hg19) of ref directory is pre-processed and indexed. *The hg38 version will be updated soon.*
-* Neopepsee requires raw FASTQ file format as input. It can be use a single or paired files.
+* STRoNGS requires raw FASTQ file format as input. It can be use a single or paired files.

  
 ### Output
-Neopepsee produces *.predicted.txt tab-delimited TXT file each HLA locus (A, B and C).
+STRoNGS produces *.typing.txt tab-delimited TXT file.

-* **transcript** : UCSC transcript id 
-* **gene** : gene symbol
-* **chr** : chromosome
-* **pos** : position
-* **ref **: reference sequence
-* **alt** : alteration sequence
-* **expr(TPM)** : expression value by TPM
-* **WT_AA** : wild type amino acid sequence
-* **MT_AA** : mutant type amino acid sequence
-* **HLA-A/B/C**
-    * **allele** : HLA allele in each gene (A, B, C)
-    * **peptide** : N-mer peptide expected to bind MHC with highest affinity (IC50)
-    * **mutLocus** : Locus with mutated amino acid
-    * **wt/mt_rank** : percentile rank score of wild/mutant peptide calculated by IEDB recommend tool
-    * **wt/mt_ic50** : IC50 score of wild/mutant peptide calculated by IEDB recommend tool
-    * **DAI** : a log ratio of the mutant to the wild-type IC50 score 
-    * **wt/mt_Immuno** :  T cell recognition (pMHC immunogenicity) score of wild/mutant peptide calculated by the T cell class I pMHC immunogenicity predictor
-    * **wt/mt_MHC** : MHC prediction score of wild/mutant peptide calculated by NetCTLpan
-    * **wt/mt_TAP** : TAP prediction score of wild/mutant peptide calculated by NetCTLpan
-    * **wt/mt_Cle** : Cleavage prediction score of wild/mutant peptide calculated by NetCTLpan
-    * **wt/mt_Comb** : Combined score of wild/mutant peptide calculated by NetCTLpan
-    * **wt/mt_hydro** : hydrophobicity score of wild/mutant peptide
-    * **wt/mt_polar** : combimation score of polarity and charge for wild/mutant peptide
-    * **wt/mt_AAPP** : AAPPs score of wild/mutant peptide
-    * **KE** : Epitope similarity search result including the closest known epitope information
-    * **Predicted** : Neopepsee’s preidcted immunogenicity score with respect to HLA types A, B, and C
-    * **Level** : classification level by statistical method
+* **Locus** : STR locus id
+* **P_Allele** : Detected STR allele by pattern typing
+* **S_Allele** : Detected STR allele by length typing
+* **Flank5** : upstream flanking region sequence with variant
+* **RepeatPattern** : Detected repeat structure with variant
+* **Flank3** : downstream flanking region sequence with variant
+* **Ratio** : Fraction of supported read for the allele in the locus
+* **#Reads** : Count of supported read for the allele in the locus
+* **TotalReads** : Total read count in the locus
+* **Representational Read ID** : Rpresentative read id

-    

 -----

Home modified by Sora Kim

Sora Kim — Tue, 24 Jan 2017 02:02:26 -0000

--- v1
+++ v2
@@ -1,8 +1,114 @@
-Welcome to your wiki!
+# **STRoNGS** #

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+A tool for profiling of STRs using next-generation sequencing data

-The wiki uses [Markdown](/p/strongs2016/wiki/markdown_syntax/) syntax.
+-----
+[TOC]
+
+-----
+
+
+
+## Installation
+
+### Requirements 
+≥ Java 1.7
+
+
+ 
+### Download and install in Unix 
+~~~~
+> wget -r https://sourceforge.net/projects/strongs2016/files/latest/download?source=files
+> tar -zxvf 
+~~~~
+
+-----
+
+
+## Usage for Windows
+[[img src=STRoNGS_guide.png alt=STRoNGSv1.0]]
+
+
+## Usage for Linux
+
+~~~~
+usage: java -jar STRoNGS-X.X.jar [options]
+~~~~
+ 
+### Required arguments 
+~~~~
+    -r, --ref   FILE  reference file
+    -1, --read1 FILE  RNA sequencing read1 file
+    -v, --vcf   FILE  VCF formatted mutation file
+    -n, --nmer  INT   predicted size of neoantigen
+~~~~
+ 
+### Optional arguments 
+
+~~~~
+    -2, --read2         FILE  RNA sequencing read2 file
+    -d, --outDir        DIR   output directory
+~~~~
+ 
+
+
+### Input
+* Reference file (hg19) of ref directory is pre-processed and indexed. *The hg38 version will be updated soon.*
+* Neopepsee requires raw FASTQ file format as input. It can be use a single or paired files.
+
+
+ 
+### Output
+Neopepsee produces *.predicted.txt tab-delimited TXT file each HLA locus (A, B and C).
+
+* **transcript** : UCSC transcript id 
+* **gene** : gene symbol
+* **chr** : chromosome
+* **pos** : position
+* **ref **: reference sequence
+* **alt** : alteration sequence
+* **expr(TPM)** : expression value by TPM
+* **WT_AA** : wild type amino acid sequence
+* **MT_AA** : mutant type amino acid sequence
+* **HLA-A/B/C**
+    * **allele** : HLA allele in each gene (A, B, C)
+    * **peptide** : N-mer peptide expected to bind MHC with highest affinity (IC50)
+    * **mutLocus** : Locus with mutated amino acid
+    * **wt/mt_rank** : percentile rank score of wild/mutant peptide calculated by IEDB recommend tool
+    * **wt/mt_ic50** : IC50 score of wild/mutant peptide calculated by IEDB recommend tool
+    * **DAI** : a log ratio of the mutant to the wild-type IC50 score 
+    * **wt/mt_Immuno** :  T cell recognition (pMHC immunogenicity) score of wild/mutant peptide calculated by the T cell class I pMHC immunogenicity predictor
+    * **wt/mt_MHC** : MHC prediction score of wild/mutant peptide calculated by NetCTLpan
+    * **wt/mt_TAP** : TAP prediction score of wild/mutant peptide calculated by NetCTLpan
+    * **wt/mt_Cle** : Cleavage prediction score of wild/mutant peptide calculated by NetCTLpan
+    * **wt/mt_Comb** : Combined score of wild/mutant peptide calculated by NetCTLpan
+    * **wt/mt_hydro** : hydrophobicity score of wild/mutant peptide
+    * **wt/mt_polar** : combimation score of polarity and charge for wild/mutant peptide
+    * **wt/mt_AAPP** : AAPPs score of wild/mutant peptide
+    * **KE** : Epitope similarity search result including the closest known epitope information
+    * **Predicted** : Neopepsee’s preidcted immunogenicity score with respect to HLA types A, B, and C
+    * **Level** : classification level by statistical method
+
+    
+
+-----
+
+
+## Example workflows
+
+
+### STRoNGS running
+
+~~~~
+java -jar STRoNGS-X.X.jar \
+    -1 sample_1.fastq \
+    -2 sample_2.fastq \
+    -r /path/reference \
+    -m /path/marker.txt
+~~~~
+
+-----
+

 [[members limit=20]]
 [[download_button]]

Home modified by Sora Kim

Sora Kim — Thu, 17 Nov 2016 06:45:57 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

Project Members:

Sora Kim (admin)