From 6ff24e84ac9c7f0e1511b3c190473db6419e3336 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 2 Oct 2018 13:39:03 +0200
Subject: [PATCH] 1_JU28_59vs17_SNP_calling.sh: add training step analysis
---
src/1_JU28_59vs17_SNP_calling.sh | 25 +++++++++++++++++++++++--
1 file changed, 23 insertions(+), 2 deletions(-)
diff --git a/src/1_JU28_59vs17_SNP_calling.sh b/src/1_JU28_59vs17_SNP_calling.sh
index edc938e..5937da1 100644
--- a/src/1_JU28_59vs17_SNP_calling.sh
+++ b/src/1_JU28_59vs17_SNP_calling.sh
@@ -1,6 +1,27 @@
#!/bin/sh
-./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" -resume -w ~/data/work/
+
+# generate training set
+ll *.gz | sed 's/.gz//g' | awk '{system("gunzip -c "$9".gz > ~/data/JU28_59vs17_SNP/data/samples/"$9)}'
+cd ~/data/JU28_59vs17_SNP/data/samples/
+~/scripts/fastq_sampler/fastq_sampler.py -i 100000 -f MR_350_clean_1.fastq -g MR_350_clean_2.fastq
+~/scripts/fastq_sampler/fastq_sampler.py -i 100000 -f MR_550_clean_1.fastq -g MR_550_clean_2.fastq
+~/scripts/fastq_sampler/fastq_sampler.py -i 100000 -f NG-10944_JU2859_bis_lib169352_5217_1_1.fastq -g NG-10944_JU2859_bis_lib169352_5217_1_2.fastq
+ll s_*.fastq | awk '{system("gzip < "$9" > "$9".gz")}'
+cd ~/projects/JU28_59vs17_SNP/
+
+# training set analysis
+
+./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/samples/*_{1,2}.fastq.gz" -resume -w ~/data/work/ --tumor "[\"NG-10944_JU2859_bis_lib169352_5217_1\"]" --normal "[\"MR_550_clean\", \"MR_350_clean\"]"
+~/scripts/sms.sh "SNP done"
+
+# real set analysis
+
+./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" -resume -w ~/data/work/ --tumor "[\"NG-10944_JU2859_bis_lib169352_5217_1\"]" --normal "[\"MR_550_clean\", \"MR_350_clean\"]"
+~/scripts/sms.sh "SNP done"
./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" --sam "results/mapping/sam/*.sam" -resume -w ~/data/work/
-./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" --sam "results/mapping/sam/*.sam" -resume -w ~/data/work/ --tumor "[\"NG-10944_JU2859_bis_lib169352_5217_1\"]" --normal "[\"MR_550_clean\"], \"MR_350_clean\"]"
+./nextflow src/SNP_calling.nf -c src/SNP_calling.config -profile docker --fasta "data/fasta/DBG2OLC-output2.fasta" --fastq "data/fastq/*_{1,2}.fastq.gz" --sam "results/mapping/sam/*.sam" -resume -w ~/data/work/ --tumor "[\"NG-10944_JU2859_bis_lib169352_5217_1\"]" --normal "[\"MR_550_clean\", \"MR_350_clean\"]"
+~/scripts/sms.sh "SNP done"
+
+
--
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