Recent changes to GS

GS modified by Giese, Sven

Giese, Sven — Thu, 25 Apr 2013 12:00:51 -0000

--- v26
+++ v27
@@ -103,7 +103,7 @@

 To filter alignments according to the features RQS (-r), gaps (-g) and mismatches (-m) just run:

- arden-filter input.sam output.sam -r value1 -m value2  - g value3  
+ arden-filter input.sam output.sam -r value1 -m value2  -g value3

WikiPage GS modified by Giese, Sven

Giese, Sven — Wed, 13 Mar 2013 14:42:13 -0000

--- v25
+++ v26
@@ -62,8 +62,8 @@
   #  | Artificial fasta
   &  | Fastq file
   @  | Mapper ID
-  bamref  | alignment REF
-  bamart  | alignment ART
+  ref  | alignment REF
+  art  | alignment ART
   +| End

 For our example the ControlFile.ini should like this:
@@ -73,12 +73,12 @@
 \#:/data/test/AR_111_21_zymamo.fasta
 &:/data/test/zymamo.fastq
 @Bow2
-bamref:/data/test/Bow2_REF_sorted.sam
-bamarg:/data/test/Bow2_ART_sorted.sam
+ref:/data/test/Bow2_REF_sorted.sam
+art:/data/test/Bow2_ART_sorted.sam
 +
 @RazerS3
-bamref:/data/test/Raz3_REF_sorted.sam
-bamarg:/data/test/Raz3_ART_sorted.sam
+ref:/data/test/Raz3_REF_sorted.sam
+art:/data/test/Raz3_ART_sorted.sam
 +
  
 After de

WikiPage GS modified by Giese, Sven

Giese, Sven — Wed, 13 Mar 2013 14:41:40 -0000

--- v24
+++ v25
@@ -93,7 +93,7 @@

-* .esam files: The files contain the alignment information extracted by ARDEN in a simpliefied "sam" format. The columns include (ReadID, Boolean indicating TP(1) or FP(0), substitutions between artificial and reference in the region spanned with the read, edit distance, read quality score, mapping quality, start alignment, end alignment number of gaps, number of mismatches)
+* .esam files: The files contain the alignment information extracted by ARDEN in a simpliefied "sam" format (see here for details)
 * results.txt: This textfile contains the results table with the overview about numerical results (senstivitiy, specificity, AUC) and all read mappers
 * ROC plots: Plots of the correspoding ROC curve for each mapper.
 * ROC tables: Tables for each mapper, where for each subclass the sensitivity, specificity and M are displayed. This table is usefull to determine an adequate quality threshold.

WikiPage GS modified by Giese, Sven

Giese, Sven — Wed, 13 Mar 2013 13:40:07 -0000

--- v23
+++ v24
@@ -6,7 +6,7 @@

 #Introduction
-For this guide we will use a very small example for a walk through. The reference genome is the sequence of Zymomonas mobilis subsp. mobilis ZM4 chromosome written to NC_006526.fna. For the read mapping step we simply simulate 10k reads of length 100 using mason  \[2] in zymamo_10k_100L.fastq (simulation just for the sake of this tutorial).
+For this guide we will use a very small example for a walk through. The reference genome is the sequence of Zymomonas mobilis subsp. mobilis ZM4 chromosome written to NC_006526.fna. For the read mapping step we simply simulate 100k reads of length 100 using mason  \[2] in zymamo_100k_100L.fastq (simulation just for the sake of this tutorial). An overview for the results of this guide is given HERE

 #Creating an artificial reference genome#
 The first step will create the artificial reference genome. The options can be seen with:

WikiPage GS modified by Giese, Sven

Giese, Sven — Wed, 13 Mar 2013 13:10:06 -0000

--- v22
+++ v23
@@ -6,7 +6,7 @@

 #Introduction
-For this guide we will use a very small example for a walk through. The data is contained in the test folder included in ARDEN download archive. The reference genome is the sequence of Zymomonas mobilis subsp. mobilis ZM4 chromosome written to NC_006526.fna. For the read mapping step we included 10k simulated reads using mason \[2] in zymamo_10k_100L.fastq
+For this guide we will use a very small example for a walk through. The reference genome is the sequence of Zymomonas mobilis subsp. mobilis ZM4 chromosome written to NC_006526.fna. For the read mapping step we simply simulate 10k reads of length 100 using mason  \[2] in zymamo_10k_100L.fastq (simulation just for the sake of this tutorial).

 #Creating an artificial reference genome#
 The first step will create the artificial reference genome. The options can be seen with: 
@@ -32,7 +32,7 @@
 #Mapping step
 For this step map the simulated reads to the reference and the created arti
 cial
-reference. Use any read mapper supporting SAM format.
+reference. Use any read mapper supporting SAM format. We chose Bowtie2 and RazerS3.

 #Sorting step
 To sort the reads the following combination of SAMtools \[2] commands can be
@@ -77,8 +77,8 @@
 bamarg:/data/test/Bow2_ART_sorted.sam
 +
 @RazerS3
-bamref:/data/test/REF_sorted.sam
-bamarg:/data/test/ART_sorted.sam
+bamref:/data/test/Raz3_REF_sorted.sam
+bamarg:/data/test/Raz3_ART_sorted.sam
 +
  
 After de
@@ -91,7 +91,9 @@
 ## Generated Output
  The program call will generate four types of output:

-* .esam files: The files contain the alignment information extracted by ARDEN in a simpliefied "sam" format.
+
+
+* .esam files: The files contain the alignment information extracted by ARDEN in a simpliefied "sam" format. The columns include (ReadID, Boolean indicating TP(1) or FP(0), substitutions between artificial and reference in the region spanned with the read, edit distance, read quality score, mapping quality, start alignment, end alignment number of gaps, number of mismatches)
 * results.txt: This textfile contains the results table with the overview about numerical results (senstivitiy, specificity, AUC) and all read mappers
 * ROC plots: Plots of the correspoding ROC curve for each mapper.
 * ROC tables: Tables for each mapper, where for each subclass the sensitivity, specificity and M are displayed. This table is usefull to determine an adequate quality threshold.

WikiPage GS modified by Giese, Sven

Giese, Sven — Tue, 12 Mar 2013 14:15:12 -0000

--- v21
+++ v22
@@ -99,9 +99,9 @@

 #Filtering (optional)

-To filter alignments according to the features RQS (-r), gaps -g) and mismatches-m) just run:
+To filter alignments according to the features RQS (-r), gaps (-g) and mismatches (-m) just run:

- arden-filter input.sam output.sam -r x -m y - g z 
+ arden-filter input.sam output.sam -r value1 -m value2  - g value3

WikiPage GS modified by Giese, Sven

Giese, Sven — Mon, 11 Mar 2013 17:32:30 -0000

--- v20
+++ v21
@@ -99,7 +99,7 @@

 #Filtering (optional)

-To filter alignments according to the features RSQ, gaps and mismatches just run:
+To filter alignments according to the features RQS (-r), gaps -g) and mismatches-m) just run:

  arden-filter input.sam output.sam -r x -m y - g z

WikiPage GS modified by Giese, Sven

Giese, Sven — Mon, 11 Mar 2013 16:54:41 -0000

--- v19
+++ v20
@@ -40,7 +40,7 @@

  samtools view -F 4 -bS input.sam | samtools sort -no - -| samtools view -h - > output.sam

-To sort the files in parallel it might be an option to use GNU parallel . The following command will convert all *.sam files in the current directory with all available cores.  \[3].
+To sort the files in parallel it might be an option to use GNU parallel  \[3]. The following command will convert all *.sam files in the current directory with all available cores.

  ls *.sam | parallel "samtools view -F 4 -bS {} | samtools sort -no - -| samtools view -h - > {.}_sorted.sam"

WikiPage GS modified by Giese, Sven

Giese, Sven — Mon, 11 Mar 2013 16:53:15 -0000

--- v18
+++ v19
@@ -17,9 +17,17 @@

  arden-create -e 1

-The following command line will produce a artificial reference with a substitution on every 21th nucleotide (-d 21). Orfs will not be protected from mutations (-o 0) and the name for the sequence is zymamo (-n). Note that the options for CreateAR are written after the first -o without blanks!
+The following command line will produce an artificial reference with a substitution on every 21th nucleotide (-d 21). Orfs will not be protected from mutations (-o 0) and the name for the sequence is zymamo (-n). It is recommended to set this name to a string without special characters. Otherwise the fasta header will be used which might not look "nice".

- arden-create /data/test/ /data/test/NC_006526.fna -o -d21-o0-nzymamo 
+ arden-create /data/test/ /data/test/NC_006526.fna -d 21 -o 0 -n zymamo 
+
+## Generated Output
+
+arden-create will generate three different types of output with the following naming convention. AR_abc_distance_referencename, where a = orf option, b = reverse unbalanced mutations option, c = random option.
+
+* Artificial Reference: A nucleotide sequence generated from the input genome.
+* Distances.txt: A file which summarizes the differences between the artificial reference and the input genome in terms of nucleotide /amino acid distribution.
+* CompleteLog.txt: A log file which traces the nucleotide / amino acid changes between artificial reference and input genome.

 #Mapping step
 For this step map the simulated reads to the reference and the created arti
@@ -32,7 +40,7 @@

  samtools view -F 4 -bS input.sam | samtools sort -no - -| samtools view -h - > output.sam

-To sort the files in parallel it might be an option to use GNU parallel   \[3].
+To sort the files in parallel it might be an option to use GNU parallel . The following command will convert all *.sam files in the current directory with all available cores.  \[3].

  ls *.sam | parallel "samtools view -F 4 -bS {} | samtools sort -no - -| samtools view -h - > {.}_sorted.sam"

WikiPage GS modified by Giese, Sven

Giese, Sven — Thu, 07 Mar 2013 14:18:11 -0000

--- v17
+++ v18
@@ -11,15 +11,15 @@
 #Creating an artificial reference genome#
 The first step will create the artificial reference genome. The options can be seen with:

- arden CreateAR
+ arden-create

 Moreover a list of examples can be printed with:

- arden CreateAR -e 1
+ arden-create -e 1

 The following command line will produce a artificial reference with a substitution on every 21th nucleotide (-d 21). Orfs will not be protected from mutations (-o 0) and the name for the sequence is zymamo (-n). Note that the options for CreateAR are written after the first -o without blanks!

- arden CreateAR /data/test/ /data/test/NC_006526.fna -o -d21-o0-nzymamo 
+ arden-create /data/test/ /data/test/NC_006526.fna -o -d21-o0-nzymamo 

 #Mapping step
 For this step map the simulated reads to the reference and the created arti
@@ -78,9 +78,25 @@
 the programm call to compare the alignments can
 be done with:

- arden analyse /data/test/ControlFile.ini /data/test/results/  
+ arden-analyze /data/test/ControlFile.ini /data/test/results/  
+
+## Generated Output
+ The program call will generate four types of output:
+
+* .esam files: The files contain the alignment information extracted by ARDEN in a simpliefied "sam" format.
+* results.txt: This textfile contains the results table with the overview about numerical results (senstivitiy, specificity, AUC) and all read mappers
+* ROC plots: Plots of the correspoding ROC curve for each mapper.
+* ROC tables: Tables for each mapper, where for each subclass the sensitivity, specificity and M are displayed. This table is usefull to determine an adequate quality threshold.
+

 #Filtering (optional)
+
+To filter alignments according to the features RSQ, gaps and mismatches just run:
+
+ arden-filter input.sam output.sam -r x -m y - g z 
+
+
+
 #References
 \[1] Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer,
 N., Marth, G., et al. (2009). The Sequence Alignment/Map for-mat and SAMtools. Bioinformatics (Oxford, England), 25(16), 2078-9. doi:10.1093/bioinformatics/btp352