Recent changes to quickstart

quickstart modified by John Archer

John Archer — Tue, 15 Feb 2022 12:25:33 -0000

--- v13
+++ v14
@@ -1,5 +1,4 @@
 [Back](https://sourceforge.net/p/csreadgen/wiki/Home/)
-
 **1. Obtaining CSReadGen**

 **1.1** A zip file (CSReadGen.zip) containing CSReadGen.jar, license, sample data and quick start can be downloaded from the Files tab of the sourceforge url: https://sourceforge.net/projects/csreadgen/.

quickstart modified by John Archer

John Archer — Tue, 15 Feb 2022 12:21:21 -0000

--- v12
+++ v13
@@ -1,4 +1,4 @@
-(first draft)
+[Back](https://sourceforge.net/p/csreadgen/wiki/Home/)

 **1. Obtaining CSReadGen**

quickstart modified by John Archer

John Archer — Wed, 17 Nov 2021 15:27:42 -0000

--- v11
+++ v12
@@ -16,7 +16,7 @@

 *java -jar CSReadGen.jar -refset path-to-ref-set -outdir path-to-out-dir*

-The varioius parameter options can be used to generated reads more specific to the users requirements. For example:
+The various parameter options can be used to generated reads more specific to the users requirements. For example:

 (i) To increase the number of reads created use the -no_of_rds parameter:

quickstart modified by John Archer

John Archer — Wed, 17 Nov 2021 15:26:00 -0000

--- v10
+++ v11
@@ -12,7 +12,7 @@

 **2. Running CSReadGen**

-**2.1** Although there are many parameters for CSReadGen, the basic command to generate one million simulated reads is:
+**2.1** Although there are many parameters for CSReadGen, the basic command to generate one million  read pairs is:

 *java -jar CSReadGen.jar -refset path-to-ref-set -outdir path-to-out-dir*

@@ -20,25 +20,27 @@

 (i) To increase the number of reads created use the -no_of_rds parameter:

-*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_rds 5000000*
+*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_pairs 5000000*

 (ii) To generate multiple replicates use the -reps parameter e.g:

-*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_rds 5000000 -reps 5*
+*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_pairs 5000000 -reps 5*

 (iii) To label each of these replicates with a condition indicator use the -ctag parameter e.g.:

-*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_rds 5000000 –reps 5 -ctag condA*
+*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_pairs 5000000 –reps 5 -ctag condA*

 (iv) To select 1000 random transcripts for over expression across the conditions use:

-*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_rds 5000000 –reps 5 -ctag condA -rnd_ovr_exp 1000*
+*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_pairs 5000000 –reps 5 -ctag condA -rnd_ovr_exp 1000*

 Each of these examples can be made more specific through the use of additional parameters such as those that specify the level of over expression required (-over_exp_lfactor and -over_exp_hfactor) and those that specify the level of general background variation within read counts between replicated (-vlow and -vhi parameters). All parameters are described below:

-*-no_of_rds*: Indicates the number of reads to be simulated. The number of reads created will be very slightly below the value specified. This is because initially read coverage is evenly distributed across all reference sequences present within the reference set, after which any user specified levels of over expression and variation are accounted for. The final numbers of reads required for each template within the reference set is then normalized based on the value of the –no_of_rds parameter, where for each template this is rounded down to the nearest integer. Default value: 1000000, maximum value: 100000000 and minimum value: 10000.
+*-no_of_pairs*: Indicates the number of pairs to be simulated. The number of pairs created will be very slightly below the value specified. This is because initially read coverage is evenly distributed across all reference sequences present within the reference set, after which any user specified levels of over expression and variation are accounted for. The final numbers of pairs required for each template within the reference set is then normalized based on the value of the –no_of_pairs parameter, where for each template this is rounded down to the nearest integer. Default value: 1000000, maximum value: 100000000 and minimum value: 10000.

 *-reps*: Specifies the number of reps to be created. Reads between replicate datasets share overall identity, as they are generated off the same reference set, but count values differ within: (i) the range of background variation (as specified by–vlow and -vhi), (ii) differentially expressed transcripts (if specified by either -rnd_ovr_exp or -usr_ovr_exp) and (iii) mismatch and indel error rates (if specified by -err_mis, -err_del and/or -err_ins). Default value: 1, maximum value: 100 and minimum value: 1.
+
+*-ctag*: a piece of text that will be added as a label to the read files e.g. condition. If reps are specified, rep number is added automatically, in this case ctag is in addition to rep number.

 *-gen_div*: The proportion of sites that will be selected for random variation sequences within the reference set. For example if 0.1 is the parameter, 10% of the sites within the reference sequences will be selected for random nucleotide alteration, after which the altered sequences will be used for read simulation. Default value: 0.0, maximum value: 1 and minimum value: 0.0.

quickstart modified by John Archer

John Archer — Tue, 09 Nov 2021 12:57:11 -0000

quickstart modified by John Archer

John Archer — Tue, 09 Nov 2021 12:57:08 -0000

--- v8
+++ v9
@@ -32,7 +32,7 @@

 (iv) To select 1000 random transcripts for over expression across the conditions use:

-*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_rds 5000000 –reps 5 -ctag condA -rndovrexp 1000*
+*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_rds 5000000 –reps 5 -ctag condA -rnd_ovr_exp 1000*

 Each of these examples can be made more specific through the use of additional parameters such as those that specify the level of over expression required (-over_exp_lfactor and -over_exp_hfactor) and those that specify the level of general background variation within read counts between replicated (-vlow and -vhi parameters). All parameters are described below:

quickstart modified by John Archer

John Archer — Mon, 08 Nov 2021 17:41:14 -0000

--- v7
+++ v8
@@ -20,19 +20,19 @@

 (i) To increase the number of reads created use the -no_of_rds parameter:

-*java -jar CSReadGen.jar -refset path-to-ref-set -outdir path-to-out-dir -noofrds 5000000*
+*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_rds 5000000*

 (ii) To generate multiple replicates use the -reps parameter e.g:

-*java -jar CSReadGen.jar -refset path-to-ref-set -outdir path-to-out-dir -noofrds 5000000 -reps 5*
+*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_rds 5000000 -reps 5*

 (iii) To label each of these replicates with a condition indicator use the -ctag parameter e.g.:

-*java -jar CSReadGen.jar -refset path-to-ref-set -outdir path-to-out-dir -noofrds 5000000 –reps 5 -ctag condA*
+*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_rds 5000000 –reps 5 -ctag condA*

 (iv) To select 1000 random transcripts for over expression across the conditions use:

-*java -jar CSReadGen.jar -refset path-to-ref-set -outdir path-to-out-dir -noofrds 5000000 –reps 5 -ctag condA -rndovrexp 1000*
+*java -jar CSReadGen.jar -ref_set path-to-ref-set -out_dir path-to-out-dir -no_of_rds 5000000 –reps 5 -ctag condA -rndovrexp 1000*

 Each of these examples can be made more specific through the use of additional parameters such as those that specify the level of over expression required (-over_exp_lfactor and -over_exp_hfactor) and those that specify the level of general background variation within read counts between replicated (-vlow and -vhi parameters). All parameters are described below:

quickstart modified by John Archer

John Archer — Fri, 05 Nov 2021 14:46:28 -0000

--- v6
+++ v7
@@ -48,6 +48,8 @@

 *-ref_set*: Specifies the path to the file containing the set of reference sequences from which reads will be simulated. This file must be in fasta or fasta.gz format and this is indicated by the –gz parameter where the default is false.

+*-out_dir*: Specifies the path to the output directory.
+
 *-rd_ln*: Specifies the length of the reads simulated. If the optional -err_ins  and -err_del parameters are used in order to introduce indel error into reads, then some minor variation around this length will occur. Default value 100: maximum value: 500, minimum value 50.

 *-insert_sz*: Specifies the size of the region that is randomly selected from a reference sequence during each read pair generation. If this region is shorter than the combined length of the paired reads, then they will overlap each. Default value 101: maximum value: 1000, minimum value 100.

quickstart modified by John Archer

John Archer — Fri, 05 Nov 2021 14:40:58 -0000

--- v5
+++ v6
@@ -54,7 +54,7 @@

 *-min_tln*: Sequences below this length within the reference set will be ignored and no reads will be simulated off of them. Default value 101: maximum value: 50000, minimum value 50.

-*-max_tln*: Sequences above this length within the reference set will be ignored and no reads will be simulated off of them. Default value 101: maximum value: 50000, minimum value 50.
+*-max_tln*: Sequences above this length within the reference set will be ignored and no reads will be simulated off of them. Default value 10000: maximum value: 50000, minimum value 50.

 *-gz*: Specifies whether or not the input reference sequences in fasta format are compressed. Default value: false. Note: all reads are outputted in .gz files regardless of this parameter.

quickstart modified by John Archer

John Archer — Fri, 05 Nov 2021 13:52:45 -0000

--- v4
+++ v5
@@ -70,7 +70,7 @@

 *-ovr_exp_lfactor*: Within each replicate the number of reads created for reference sequences (following even coverage) that have been selected for over expression will be increased by a factor falling between this value and the upper limit specified by -over_exp_hfactor. For example, if 70 reads were required for a selected reference sequences to provide even coverage, relative to other reference sequences, then this value would be increase to 70 + (70 * 2) if 2 was the selected for a particular replicated. These values do not include random background variation which is added in accordance with -vlow  and –vhi parameters. Default value 1: maximum value: 50, minimum value 1.

-*-ovr_exp_hfactor*: This specifies the upper pound described for -ovr_exp_lfactor.
+*-ovr_exp_hfactor*: This specifies the upper bound described for -ovr_exp_lfactor.


 **3. Sample Data**