full assembly script-Chia

svn path=/; revision=618

diff --git a/Personnel/albader/assembley.sh b/Personnel/albader/assembley.sh
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+++ b/Personnel/albader/assembley.sh
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+#!/bin/bash
+#$ -q uncia
+
+# two velveth scripts, for 2 different kmer size
+
+velveth assembly_67/ 67 -short -fastq /lemma/albader/chia/single-Salba-D3-AB6.trimmed.fastq -shortpaired -fastq -seperate /lemma/albader/chia/forward-Salba-D3-AB6.trimmed.fastq /lemma/albader/chia/revers-Salba-D3-AB6.trimmed.fastq
+velveth assembly_71/ 71 -short -fastq /lemma/albader/chia/single-Salba-D3-AB6.trimmed.fastq -shortpaired -fastq -seperate /lemma/albader/chia/forward-Salba-D3-AB6.trimmed.fastq /lemma/albader/chia/revers-Salba-D3-AB6.trimmed.fastq
+
+#two velvetg scripts, for 2 different kmer size
+
+velvetg assembly_67/ -read_trkr yes -unused_reads yes
+velvetg assembly_71/ -read_trkr yes -unused_reads yes
+
+#Oases scripts for both kmer size
+oases assembly_67/ -cov_cutoff 10 -edgeFractionCutoff 0.01 -min_trans_lgth 201
+oases assembly_71/ -cov_cutoff 10 -edgeFractionCutoff 0.01 -min_trans_lgth 201
+
+#Merging Asemblies with velvetg velveth and oasis
+velveth mergerd_assemblies/ 67 -long assembly*/transcripts.fa
+velvetg mergerd_assemblies/ -read_trkr yes -conservelong yes
+oases mergerd_assemblies/ -merge yes -min_trans_lgth 201
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