SSPACE - Revision history

Rf at 14:02, 13 October 2016

2016-10-13T14:02:02Z

2016-10-13T13:54:57Z

2016-10-13T13:48:28Z

2016-10-13T13:44:20Z

2016-10-13T13:43:13Z

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2016-09-01T16:03:35Z

2016-09-01T15:12:01Z

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 * Bowtie is also usually the preferred aligner.
 * the apir of reads ... no expalanation needed, this is obvious.
-* we then get an integer and an floating point value. They go together. They relate to max. distance between reads.
+* we then get an integer and an floating point value. They go together. They relate to insert size error. 0.25 on 200 would be 50 bp on eith side of the insert size. Insert size is usually a library value. For Miseq, 200 and 0.25 seem reasonable.
 * The FR is what you would normally want ... i.e. reads are in forward and reverse order.

@@ Line 13: / Line 13: @@
   lib1 bowtie SRR001665_1.fastq.gz SRR001665_2.fastq.gz 200 0.25 FR
-The FR is what you would normally want ... i.e. reads are in forward and reverse order. Bowtie is also usually the preferred aligner.
+<ins>Explanation</ins>:
 There is one line per pair of short read files. Note that contigs / scaffolds file one is seeking to improve is not mentioned, this is becuase it falls outside, and should appear in the SSPACE.pl command line, specified through the '''-s''' option. Here is an example command line:

@@ Line 24: / Line 24: @@
 * '''-k''', the default is already 5, it's the minimum number of links required for a contig pair to be considered.
 * '''-a''', when two contigs are being combined to form another, this is the maximum overlap ratio they are allowed have for the contig. 0.7 seems good.
 = Manual =

@@ Line 22: / Line 22: @@
 * '''-l''', libraries file, aka configuration file.
 * '''-s''', the reference file
-* '''-k''', the default is already 5, it's the minimum number of links required
+* '''-k''', the default is already 5, it's the minimum number of links required for a contig pair to be considered.
 * '''-a''', when two contigs are being combined to form another, this is the maximum overlap ratio they are allowed have for the contig. 0.7 seems good.

@@ Line 22: / Line 22: @@
 * '''-l''', libraries file, aka configuration file.
 * '''-s''', the reference file
-* '''-k''', the default is already 5,
+* '''-k''', the default is already 5, it's the minimum number of links required
 = Manual =

← Older revision		Revision as of 13:38, 13 October 2016
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	SSPACE.pl -l libraries.txt -s contigs_abyss.fasta -k 5 -a 0.7 -x 0 -b ecoli_scafs_next		SSPACE.pl -l libraries.txt -s contigs_abyss.fasta -k 5 -a 0.7 -x 0 -b ecoli_scafs_next
		+
		+	<ins>Explanation</ins>:
		+	* '''-l''', libraries file, aka configuration file.
		+	* '''-s''', the reference file
		+	* '''-k''', the default is already 5,

	= Manual =		= Manual =

@@ Line 9: / Line 9: @@
   module load SSPACE
-SSPACE needs a configuration file before being run, speified b the '''-l''' option. This file specifies what the input to the program should be. Here is an example:
+SSPACE needs a configuration file before being run, specified by the '''-l''' option. This file specifies what the input to the program should be. Here is an example:
   lib1 bowtie SRR001665_1.fastq.gz SRR001665_2.fastq.gz 200 0.25 FR

← Older revision		Revision as of 16:03, 1 September 2016
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	Additional information about the input, output and general process of the		Additional information about the input, output and general process of the
	script can be found in the README file.		script can be found in the README file.
		+
		+	= Installation Notes =
		+
		+	* You need to have Perl4::CoreLibs installed, for the "require(getopts.pl)" line. This is easily done with cpanm.