Recent changes to manual

manual modified by Hayan Lee

Hayan Lee — Fri, 21 Nov 2014 16:05:39 -0000

--- v28
+++ v29
@@ -35,6 +35,10 @@
     run_readsim.ecoli.nanopore.sh  
     run_readsim.ecoli.pacbio_ec.sh
     run_readsim.ecoli.pacbio.sh
+    run_readsim.ecoli.perfect.sh
+    run_readsim.ecoli.uniform.sh
+
+
     readsim-1.0/example/script$ ./run_readsim.ecoli.pacbio.sh 
     ================================================================================
                              Read Simulator for Long Reads

manual modified by Hayan Lee

Hayan Lee — Fri, 21 Nov 2014 06:47:07 -0000

--- v27
+++ v28
@@ -73,7 +73,7 @@
 * * *
 # Settings for Long Reads Sequencing Technology  #

-### Pacbio 
+## Pacbio 
 * Average read length : 5,000 bp
 * Read distribution : exponential distribution
 * Coverage : 10x
@@ -81,7 +81,7 @@
 * Average error rate for insertion : 12%
 * Average error rate for deletion : 2%

-### Pacbio Error Corrected
+## Pacbio Error Corrected
 * Average read length : 5,000 bp
 * Read distribution : exponential distribution
 * Coverage : 10x
@@ -89,7 +89,7 @@
 * Average error rate for insertion : 0.33%
 * Average error rate for deletion : 0.33%

-### Nanopore
+## Nanopore
 * Average read length : 100,000 bp
 * Read distribution : normal distribution
 * Coverage : 10x

manual modified by Hayan Lee

Hayan Lee — Fri, 21 Nov 2014 06:46:15 -0000

--- v26
+++ v27
@@ -18,7 +18,7 @@

 * * *
-# Simple Start Using Script  #
+# Start Using Simple Script  #

 In script directory there are 3 scripts; each is for pacbio, pacbio_ec and nanopore.
 Included script gives you a simple and good start.
@@ -70,8 +70,8 @@
     [INFO:010] Total 11367 reads are generated; 5669 is forward, 5698 is reversed

-
-## Settings for Long Reads Sequencing Technology  ##
+* * *
+# Settings for Long Reads Sequencing Technology  #

 ### Pacbio 
 * Average read length : 5,000 bp
@@ -98,43 +98,46 @@
 * Average error rate for deletion : 3%

+* * *
+# Inside the Script  #

-## Inside the Script  ##
+## dnasim.py (for heterozygous polyploidy genome) ##

-This is the script for Pacbio
+    ../../src/dnasim.py --ploidy 10 --het 0.05 --pre [prefix]  [ref]
+    ../../src/dnasim.py --ploidy 10 --het 0.05 --pre NC_000913 NC_000913.fna
+
+* ploidy
+* het - heterozygous level, 0.05 means 5% difference
+
+
+## readsim.py (for reads simulation) ##
+
+The main script. When you run with your own command or fix the script, please make sure the path is correct. This is the script for Pacbio

     for l in 2000; do
       for c in 5; do 
-
         ../../src/readsim.py sim fa \
         --ref NC_000913.fna \
         --pre NC_000913.pacbio.reads \
         --rev_strd on \
         --tech pacbio_ec --read_mu $l --cov_mu $c
-
       done;
     done;

-* readsim.py - The main script. When you run with your own command or fix the script, please make sure the path is correct.
+
 * sim - The major command, meaning that we will simulate reads
-    * fa - generate a base only reads file. You will see .fasta as a result
-    * fq - generate a base and quality valued in the same file. You will see .fastq as a result
-    * fafq - generate two base reads and quality value file separately. You will see .fa and .fq file as results.
-
+    + fa - generate a base only reads file. You will see .fasta as a result
+    + fq - generate a base and quality valued in the same file. You will see .fastq as a result
+    + fafq - generate two base reads and quality value file separately. You will see .fa and .fq file as results.
 * ref - Reference genome. When you run with your own command or fix the script, please make sure the path is correct
-
 * pre - The prefix. The last file name will be prefix.{fast|fastq|fa|fq}
-
 * rev_strd - on | off, 'on' means create backward strands as well as forward strands, randomly half and half. 'off' means no backward strands, every read is forward strand.
-
 * tech - The sequencing technology that you want to simulate. We do support pacbio, pacbio_ec (pacbio error corrected) and nanopore
-
 * read_mu - The average on read length
-
 * cov_mu - The overall coverage

-## More Options ##
+### More Options ###

 * read_mu - The average on read length
 * read_dist - The overall distribution of read length. Choose among {uniform, normal, exp}. It also can take a file, in which each line has a length of a read. The read length file can get the simulated reads more realistic(v1.5). 
@@ -144,4 +147,3 @@
 * err_del_mu - The average on deletion rate

-

manual modified by Hayan Lee

Hayan Lee — Fri, 21 Nov 2014 06:32:21 -0000

--- v25
+++ v26
@@ -20,10 +20,10 @@
 * * *
 # Simple Start Using Script  #

-* In script directory there are 3 scripts; each is for pacbio, pacbio_ec and nanopore.
-* Included script gives you a simple and good start.
-* The script will run around 5-10 min, depending on your hardware specification. 
-* To get the result, follow the steps.   
+In script directory there are 3 scripts; each is for pacbio, pacbio_ec and nanopore.
+Included script gives you a simple and good start.
+The script will run around 5-10 min, depending on your hardware specification. 
+To get the result, follow the steps.   

     readsim-1.6$ cd example/
@@ -74,7 +74,7 @@
 ## Settings for Long Reads Sequencing Technology  ##

 ### Pacbio 
-* Average read length : 2,000 bp
+* Average read length : 5,000 bp
 * Read distribution : exponential distribution
 * Coverage : 10x
 * Average error rate for substitution : 1%
@@ -82,7 +82,7 @@
 * Average error rate for deletion : 2%

 ### Pacbio Error Corrected
-* Average read length : 2,000 bp
+* Average read length : 5,000 bp
 * Read distribution : exponential distribution
 * Coverage : 10x
 * Average error rate for substitution : 0.33%
@@ -90,7 +90,7 @@
 * Average error rate for deletion : 0.33%

 ### Nanopore
-* Average read length : 50,000 bp
+* Average read length : 100,000 bp
 * Read distribution : normal distribution
 * Coverage : 10x
 * Average error rate for substitution : 3%

manual modified by Hayan Lee

Hayan Lee — Fri, 21 Nov 2014 06:29:20 -0000

--- v24
+++ v25
@@ -4,55 +4,71 @@
 Please use this link to download the latest version.

 [[download_button]]
+
 * * *
 # Installation #
-    $ tar xvfz readsim-1.0.tar.gz 
-    $ cd readsim-1.0
-    readsim-1.0$ ls
-    example    script    src  
+    $ tar xvfz readsim-1.x.tar.gz 
+    $ cd readsim-1.x
+    readsim-1.x$ ls
+    example   src  

 * Download the latest version.
 + Extract the tar file.
-+ If successful, you will see readsim-1.0 directory. 
++ If successful, you will see readsim-1.x directory. 

 * * *
 # Simple Start Using Script  #

-In script directory there are 3 scripts; each is for pacbio, pacbio_ec and nanopore.
+* In script directory there are 3 scripts; each is for pacbio, pacbio_ec and nanopore.
+* Included script gives you a simple and good start.
+* The script will run around 5-10 min, depending on your hardware specification. 
+* To get the result, follow the steps.   

-    readsim-1.0$ cd script/
-    readsim-1.0/script$ ls
+
+    readsim-1.6$ cd example/
+    readsim-1.6/example$ ls
+    ecoli  pacbio.p5-c3.len.dist  script
+    readsim-1.6$ cd script/
+    readsim-1.6/example/script$ ls
+    run_dnasim.ecoli.sh  
+    run_readsim.ecoli.nanopore.sh  
+    run_readsim.ecoli.pacbio_ec.sh
     run_readsim.ecoli.pacbio.sh
-    run_readsim.ecoli.pacbio_ec.sh
-    run_readsim.ecoli.nanopore.sh
-    readsim-1.0/script$ ./run_readsim.ecoli.pacbio.sh 
-    ===============================================================
-                             Read Simulator for PacBio
- 
-    FASTA file path: ../NC_000913.fna
+    readsim-1.0/example/script$ ./run_readsim.ecoli.pacbio.sh 
+    ================================================================================
+                             Read Simulator for Long Reads
+
+    Sequencing Technology : pacbio
+    FASTA file path : NC_000913.fna
     Reads : mean(2000bp) distribution(exp)
-    Coverage : mean(5x)
+    Coverage : mean(5.0x)
     Mutation (Substitution) : mean(1.0%)
     Mutation (Insertion)    : mean(12.0%)
     Mutation (Deletion)     : mean(2.0%)
     ================================================================================
-    [INFO:001] 70 bases per line, prob of reads is 0.0025 
-    [INFO:003] NC_000913.pacbio.reads.fa are created
-    [INFO:009] position 100000 has been processed.
-    [INFO:009] position 200000 has been processed.
+    [INFO:002] 2014-11-21 01:26:32 reading NC_000913.fna
+    [INFO:002] 2014-11-21 01:26:32 done.
+    [INFO:002] 2014-11-21 01:26:32 generating length given distribution.
+    [INFO:003] 2014-11-21 01:26:32 NC_000913.pacbio.reads.fa is created
+    [INFO:012] 2014-11-21 01:26:32 position 4896 has been processed. (0.00x)
+    [INFO:012] 2014-11-21 01:26:34 position 1000417 has been processed. (0.22x)
+    [INFO:012] 2014-11-21 01:26:36 position 2000480 has been processed. (0.43x)
+    [INFO:012] 2014-11-21 01:26:37 position 3001390 has been processed. (0.65x)
+    [INFO:012] 2014-11-21 01:26:39 position 4001424 has been processed. (0.86x)
+    [INFO:012] 2014-11-21 01:26:41 position 5001934 has been processed. (1.08x)
+    [INFO:012] 2014-11-21 01:26:42 position 6000558 has been processed. (1.29x)
+
     .
     .
     .
-    readsim-1.0/script$ cd ../example/ecoli/
-    readsim-1.0/example/ecoli$ ls
-    NC_000913.fna
-    NC_000913.nanopore.reads.fasta
+    [INFO:012] 2014-11-21 01:27:06 position 20000187 has been processed. (4.31x)
+    [INFO:012] 2014-11-21 01:27:07 position 21000389 has been processed. (4.53x)
+    [INFO:012] 2014-11-21 01:27:09 position 22000240 has been processed. (4.74x)
+    [INFO:012] 2014-11-21 01:27:11 position 23003796 has been processed. (4.96x)
+    [INFO:012] 2014-11-21 01:27:11 position 23199876 has been processed. (5.00x)
+    [INFO:010] Total 11367 reads are generated; 5669 is forward, 5698 is reversed

-
-* Included script gives you a simple and good start.
-* The script will run around 5-10 min, depending on your hardware specification. 
-* To get the result, follow the steps.   

 ## Settings for Long Reads Sequencing Technology  ##
@@ -129,4 +145,3 @@

-

WikiPage manual modified by Hayan Lee

Hayan Lee — Wed, 16 Jan 2013 20:26:51 -0000

--- v23
+++ v24
@@ -121,7 +121,7 @@
 ## More Options ##

 * read_mu - The average on read length
-* read_dist - The overall distribution of read length. Choose among {uniform, normal, exp} 
+* read_dist - The overall distribution of read length. Choose among {uniform, normal, exp}. It also can take a file, in which each line has a length of a read. The read length file can get the simulated reads more realistic(v1.5). 
 * cov_mu - The overall coverage
 * err_sub_mu - The average on substitution rate
 * err_in_mu - The average on insertion rate

WikiPage manual modified by Hayan Lee

Hayan Lee — Sun, 18 Nov 2012 21:42:58 -0000

--- v22
+++ v23
@@ -111,7 +111,7 @@
 
 * rev_strd - on | off, 'on' means create backward strands as well as forward strands, randomly half and half. 'off' means no backward strands, every read is forward strand.
 
-* tech - The sequencing technology that you want to simulate. We do support pacbio and nanopore.
+* tech - The sequencing technology that you want to simulate. We do support pacbio, pacbio_ec (pacbio error corrected) and nanopore
 
 * read_mu - The average on read length

WikiPage manual modified by Hayan Lee

Hayan Lee — Fri, 16 Nov 2012 21:02:14 -0000

--- v21
+++ v22
@@ -26,7 +26,7 @@
     run_readsim.ecoli.pacbio.sh
     run_readsim.ecoli.pacbio_ec.sh
     run_readsim.ecoli.nanopore.sh
-    readsim-1.0/script$ ./run_readsim.pacbio.ecoli.sh 
+    readsim-1.0/script$ ./run_readsim.ecoli.pacbio.sh 
     ===============================================================
                              Read Simulator for PacBio
  
@@ -53,6 +53,33 @@
 * Included script gives you a simple and good start.
 * The script will run around 5-10 min, depending on your hardware specification. 
 * To get the result, follow the steps.   
+
+
+## Settings for Long Reads Sequencing Technology  ##
+
+### Pacbio 
+* Average read length : 2,000 bp
+* Read distribution : exponential distribution
+* Coverage : 10x
+* Average error rate for substitution : 1%
+* Average error rate for insertion : 12%
+* Average error rate for deletion : 2%
+
+### Pacbio Error Corrected
+* Average read length : 2,000 bp
+* Read distribution : exponential distribution
+* Coverage : 10x
+* Average error rate for substitution : 0.33%
+* Average error rate for insertion : 0.33%
+* Average error rate for deletion : 0.33%
+
+### Nanopore
+* Average read length : 50,000 bp
+* Read distribution : normal distribution
+* Coverage : 10x
+* Average error rate for substitution : 3%
+* Average error rate for insertion : 3%
+* Average error rate for deletion : 3%

WikiPage manual modified by Hayan Lee

Hayan Lee — Fri, 16 Nov 2012 20:53:59 -0000

--- v20
+++ v21
@@ -58,19 +58,17 @@
 
 ## Inside the Script  ##
 
-    for l in 5000; do
+This is the script for Pacbio
+
+    for l in 2000; do
       for c in 5; do 
 
-        mkdir l$l.c$c.e1
-        cd l$l.c$c.e1
-
-        ../../../src/readsim.py sim fa \
-        --ref ../NC_000913.fna \
+        ../../src/readsim.py sim fa \
+        --ref NC_000913.fna \
         --pre NC_000913.pacbio.reads \
         --rev_strd on \
         --tech pacbio_ec --read_mu $l --cov_mu $c
 
-        cd ..
       done;
     done;
 
@@ -96,7 +94,7 @@
 ## More Options ##
 
 * read_mu - The average on read length
-* read_dist - The overall distribution of read length. Choose among {normal, exp, poisson} 
+* read_dist - The overall distribution of read length. Choose among {uniform, normal, exp} 
 * cov_mu - The overall coverage
 * err_sub_mu - The average on substitution rate
 * err_in_mu - The average on insertion rate

WikiPage manual modified by Hayan Lee

Hayan Lee — Fri, 16 Nov 2012 20:51:02 -0000

--- v19
+++ v20
@@ -19,21 +19,25 @@
 * * *
 # Simple Start Using Script  #
 
+In script directory there are 3 scripts; each is for pacbio, pacbio_ec and nanopore.
+
     readsim-1.0$ cd script/
     readsim-1.0/script$ ls
-    run_readsim_5000.ecoli.sh
-    readsim-1.0/script$ ./run_readsim_5000.ecoli.sh 
+    run_readsim.ecoli.pacbio.sh
+    run_readsim.ecoli.pacbio_ec.sh
+    run_readsim.ecoli.nanopore.sh
+    readsim-1.0/script$ ./run_readsim.pacbio.ecoli.sh 
     ===============================================================
                              Read Simulator for PacBio
-    
+ 
     FASTA file path: ../NC_000913.fna
-    Reads : mean(5000bp) distribution(exp)
-    Coverage : mean(5x) distribution(poisson)
-    Mutation (Substitution) : mean(0.33%) distribution(normal)
-    Mutation (Insertion)    : mean(0.33%) distribution(normal)
-    Mutation (Deletion)     : mean(0.33%) distribution(normal)
-    ===============================================================
-    [INFO:001] 70 bases per line, prob of reads is 0.001 
+    Reads : mean(2000bp) distribution(exp)
+    Coverage : mean(5x)
+    Mutation (Substitution) : mean(1.0%)
+    Mutation (Insertion)    : mean(12.0%)
+    Mutation (Deletion)     : mean(2.0%)
+    ================================================================================
+    [INFO:001] 70 bases per line, prob of reads is 0.0025 
     [INFO:003] NC_000913.pacbio.reads.fa are created
     [INFO:009] position 100000 has been processed.
     [INFO:009] position 200000 has been processed.
@@ -42,11 +46,8 @@
     .
     readsim-1.0/script$ cd ../example/ecoli/
     readsim-1.0/example/ecoli$ ls
-    l5000.c5.e1/   NC_000913.fna
-    readsim-1.0/example/ecoli$ cd l5000.c5.e1/
-    readsim-1.0/example/ecoli/l5000.c5.e1$ ls
-    NC_000913.pacbio.reads.fasta
-
+    NC_000913.fna
+    NC_000913.nanopore.reads.fasta
 
 
 * Included script gives you a simple and good start.
@@ -97,13 +98,9 @@
 * read_mu - The average on read length
 * read_dist - The overall distribution of read length. Choose among {normal, exp, poisson} 
 * cov_mu - The overall coverage
-* cov_dist - The overall coverage
 * err_sub_mu - The average on substitution rate
-* err_sub_dist - The overall distribution of substitution. Choose among {normal, exp, poisson} 
 * err_in_mu - The average on insertion rate
-* err_in_dist - The overall distribution of insertion. Choose among {normal, exp, poisson} 
 * err_del_mu - The average on deletion rate
-* err_del_dist - The overall distribution of deletion. Choose among {normal, exp, poisson}