Casuarina SSR - Revision history

Raj: /* Mine for repeat motifs */

2011-12-29T05:36:09Z

Mine for repeat motifs

← Older revision		Revision as of 05:36, 29 December 2011
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	Number of sequences containing more than 1 SSR: 30		Number of sequences containing more than 1 SSR: 30
	Number of SSRs present in compound formation: 24		Number of SSRs present in compound formation: 24

			Distribution to different repeat type classes
			---------------------------------------------

			Unit size Number of SSRs
			Di 217
			Tri 141
			Tetra 25

	</pre>		</pre>

	===Design Primers===		===Design Primers===

2011-12-29T05:35:36Z

Mine for repeat motifs

← Older revision		Revision as of 05:35, 29 December 2011
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	===Mine for repeat motifs===		===Mine for repeat motifs===
			* Param:
			<pre>
			Definement of microsatellites (unit size / minimum number of repeats): (2/7) (3/5) (4/4)
			</pre>
			* Stat
			<pre>
			Total number of sequences examined: 4285
			Total size of examined sequences (bp): 3253599
			Total number of identified SSRs: 383
			Number of SSR containing sequences: 347
			Number of sequences containing more than 1 SSR: 30
			Number of SSRs present in compound formation: 24
			</pre>

	===Design Primers===		===Design Primers===

2011-12-29T05:17:07Z

Generate statistics

← Older revision		Revision as of 05:17, 29 December 2011
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	** ID Named		** ID Named
	* Distribution of length in contigs: 220-500: 546 \| 500-1000: 3119 \| 1000-1500: 529 \| >1500: 98		* Distribution of length in contigs: 220-500: 546 \| 500-1000: 3119 \| 1000-1500: 529 \| >1500: 98
			* Trimmed Sequences: '''4285'''

	===Mine for repeat motifs===		===Mine for repeat motifs===

	===Design Primers===		===Design Primers===

2011-12-29T05:08:09Z

Generate statistics

← Older revision		Revision as of 05:08, 29 December 2011
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	===Generate statistics===		===Generate statistics===
	* Distribution of length in contigs:
	* Distribution of length in singlets:
	* Final number of sequence		* Final number of sequence
	** Param: Trimmed off the <220bp \| Trimmed off the N>20%		** Param: Trimmed off the <220bp \| Trimmed off the N>20%
	** ID Named		** ID Named
			* Distribution of length in contigs: 220-500: 546 \| 500-1000: 3119 \| 1000-1500: 529 \| >1500: 98

	===Mine for repeat motifs===		===Mine for repeat motifs===

	===Design Primers===		===Design Primers===

2011-12-29T04:51:02Z

Generate statistics

← Older revision		Revision as of 04:51, 29 December 2011
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	* Distribution of length in singlets:		* Distribution of length in singlets:
	* Final number of sequence		* Final number of sequence
	** Param: Trimmed off the <220bp \| Trimmed off the N>5%		** Param: Trimmed off the <220bp \| Trimmed off the N>20%
	** ID Named		** ID Named

2011-12-29T04:19:01Z

Develop unigenes

2011-12-29T04:00:42Z

Develop unigenes

← Older revision		Revision as of 04:00, 29 December 2011
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	===Develop unigenes===		===Develop unigenes===
	* TGICL is used		* TGICL is used
	** Param:		** Param: Left to default
	<pre>		<pre>
	# -l miminum overlap length (default 40)		# -l miminum overlap length (default 40)

2011-12-29T04:00:16Z

Develop unigenes

← Older revision		Revision as of 04:00, 29 December 2011
Line 29:		Line 29:
	===Develop unigenes===		===Develop unigenes===
	* TGICL is used		* TGICL is used
	* Contigs :		** Param:
	* Singlets:		<pre>
			# -l miminum overlap length (default 40)
			# -M ignore lower-case masking in <fasta_db> sequences
			# -p minimum percent identity for overlaps <PID> (default 94)
			</pre>
			* Contigs : '''3947'''
			* Singlets: '''475'''

	===Generate statistics===		===Generate statistics===

2011-12-29T03:52:36Z

Filter the sequence

← Older revision		Revision as of 03:52, 29 December 2011
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	** Param: Trimmed off the <220bp \| Trimmed off the N>5%		** Param: Trimmed off the <220bp \| Trimmed off the N>5%
	** ID Named		** ID Named

	~~===Filter the sequence===~~

	===Mine for repeat motifs===		===Mine for repeat motifs===

	===Design Primers===		===Design Primers===

2011-12-29T03:52:15Z

Generate statistics

← Older revision		Revision as of 03:52, 29 December 2011
Line 33:		Line 33:

	===Generate statistics===		===Generate statistics===
			* Distribution of length in contigs:
			* Distribution of length in singlets:
			* Final number of sequence
			** Param: Trimmed off the <220bp \| Trimmed off the N>5%
			** ID Named

	===Filter the sequence===		===Filter the sequence===