From: albader <albader@localhost>
Date: Thu, 19 Feb 2015 19:01:08 +0000 (+0000)
Subject: updated assembly scripts $ test
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=af530f82eabd9a294d06f6e03ee9429c0d22857d;p=old-jaiswallab-svn%2F.git

updated assembly scripts $ test

svn path=/; revision=619
---

diff --git a/Personnel/albader/nb_assembly.sh b/Personnel/albader/nb_assembly.sh
new file mode 100644
index 0000000..a04c06e
--- /dev/null
+++ b/Personnel/albader/nb_assembly.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+#$ -q samwise
+
+# two velveth scripts, for 2 different kmer size
+
+velveth assembly_67/ 67 -short -fastq assembely_ready_single.trimmed.fastq -shortpaired -fastq -seperate assembely_ready_R1.trimmed.fastq assembely_ready_R2.trimmed.fastq
+velveth assembly_71/ 71 -short -fastq assembely_ready_single.trimmed.fastq -shortpaired -fastq -seperate assembely_ready_R1.trimmed.fastq assembely_ready_R2.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
diff --git a/Personnel/albader/nb_assembly.test.sh b/Personnel/albader/nb_assembly.test.sh
new file mode 100755
index 0000000..91151f0
--- /dev/null
+++ b/Personnel/albader/nb_assembly.test.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+#$ -q samwise
+
+# two velveth scripts, for 2 different kmer size
+
+velveth assemblytest_67/ 67 -short -fastq 400k_reads_single.trimmed.fastq  -shortpaired -fastq -seperate 400k_reads_R1.trimmed.fastq 400k_reads_R2.trimmed.fastq
+velveth assemblytest_71/ 71 -short -fastq 400k_reads_single.trimmed.fastq  -shortpaired -fastq -seperate 400k_reads_R1.trimmed.fastq 400k_reads_R2.trimmed.fastq 
+
+#two velvetg scripts, for 2 different kmer size
+
+velvetg assemblytest_67/ -read_trkr yes -unused_reads yes
+velvetg assemblytest_71/ -read_trkr yes -unused_reads yes
+
+#Oases scripts for both kmer size
+
+oases assemblytest_67/ -cov_cutoff 10 -edgeFractionCutoff 0.01 -min_trans_lgth 201
+oases assemblytest_71/ -cov_cutoff 10 -edgeFractionCutoff 0.01 -min_trans_lgth 201
+
+#Merging Asemblies with velvetg velveth and oasis
+
+velveth mergerd_assemblies_test/ 67 -long assembly*/transcripts.fa
+velvetg mergerd_assemblies_test/ -read_trkr yes -conservelong yes
+oases mergerd_assemblies_test/ -merge yes -min_trans_lgth 201