From 0ea3dbdbfd43601fb9c3dc6dc7328f6ccee11dfa Mon Sep 17 00:00:00 2001 From: albader Date: Thu, 19 Feb 2015 18:36:19 +0000 Subject: [PATCH] full assembly script-Chia svn path=/; revision=618 --- Personnel/albader/assembley.sh | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 Personnel/albader/assembley.sh diff --git a/Personnel/albader/assembley.sh b/Personnel/albader/assembley.sh new file mode 100644 index 0000000..408057b --- /dev/null +++ b/Personnel/albader/assembley.sh @@ -0,0 +1,21 @@ +#!/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 \ No newline at end of file -- 2.34.1