adding my first shell scripts for chia (round 1)

svn path=/; revision=616

diff --git a/Personnel/albader/.gitignore b/Personnel/albader/.gitignore
deleted file mode 100644 (file)
index e69de29..0000000

diff --git a/Personnel/albader/chia_cp.sh b/Personnel/albader/chia_cp.sh
new file mode 100755 (executable)
index 0000000..8ef4d12
--- /dev/null
+++ b/Personnel/albader/chia_cp.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+#$ -cwd
+cp -r /lemma/genizam/CHIA/fastq/salba/Sample_lane4-index08-ACTTGA-Salba-D3-AB6-R1/ /lemma/albader/chia 
+cp -r /lemma/genizam/CHIA/fastq/salba/Sample_lane4-index16-CCGTCC-Salba-D3-AB6-R2/ /lemma/albader/chia
+cp -r /lemma/genizam/CHIA/fastq/salba/Sample_lane4-index24-GGTAGC-Salba-D3-AB6-R3/ /lemma/albader/chia
+
+
+

diff --git a/Personnel/albader/chia_sickle.sh b/Personnel/albader/chia_sickle.sh
new file mode 100755 (executable)
index 0000000..e1f1602
--- /dev/null
+++ b/Personnel/albader/chia_sickle.sh
@@ -0,0 +1,13 @@
+0#!/bin/bash
+#$ -cwd
+/raid1/home/mcb/genizam/sickle-master/sickle pe -f lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R1_001.fastq -r lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R2_001.fastq -t sanger -q 20 -o lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R1_001.trimmed.fastq -p lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R2_001.trimmed.fastq -s lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004.trimmed.single1.fastq
+/raid1/home/mcb/genizam/sickle-master/sickle pe -f lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R1_002.fastq -r lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R2_002.fastq -t sanger -q 20 -o lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R1_002.trimmed.fastq -p lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R2_002.trimmed.fastq -s lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004.trimmed.single2.fastq
+/raid1/home/mcb/genizam/sickle-master/sickle pe -f lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R1_003.fastq -r lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R2_003.fastq -t sanger -q 20 -o lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R1_003.trimmed.fastq -p lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R2_003.trimmed.fastq -s lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004.trimmed.single3.fastq
+/raid1/home/mcb/genizam/sickle-master/sickle pe -f lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R1_001.fastq -r lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R2_001.fastq -t sanger -q 20 -o lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R1_001.trimmed.fastq -p lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R2_001.trimmed.fastq -s lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004.trimmed.single1.fastq
+/raid1/home/mcb/genizam/sickle-master/sickle pe -f lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R1_002.fastq -r lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R2_002.fastq -t sanger -q 20 -o lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R1_002.trimmed.fastq -p lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R2_002.trimmed.fastq -s lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004.trimmed.single2.fastq
+/raid1/home/mcb/genizam/sickle-master/sickle pe -f lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R1_003.fastq -r lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R2_003.fastq -t sanger -q 20 -o lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R1_003.trimmed.fastq -p lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R2_003.trimmed.fastq -s lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004.trimmed.single3.fastq
+/raid1/home/mcb/genizam/sickle-master/sickle pe -f lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_001.fastq -r lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R2_001.fastq -t sanger -q 20 -o lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_001.trimmed.fastq -p lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R2_001.trimmed.fastq -s lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_001.trimmed.single1.fastq
+/raid1/home/mcb/genizam/sickle-master/sickle pe -f lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_002.fastq -r lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R2_002.fastq -t sanger -q 20 -o lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_002.trimmed.fastq -p lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R2_002.trimmed.fastq -s lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004.trimmed.single2.fastq
+/raid1/home/mcb/genizam/sickle-master/sickle pe -f lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_003.fastq -r lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R2_003.fastq -t sanger -q 20 -o lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_003.trimmed.fastq -p lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R2_003.trimmed.fastq -s lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004.trimmed.single3.fastq
+
+

diff --git a/Personnel/albader/concat.sh b/Personnel/albader/concat.sh
new file mode 100755 (executable)
index 0000000..bb83678
--- /dev/null
+++ b/Personnel/albader/concat.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+#$ -cwd
+
+cat l*R1_00*.trimmed.fastq > forward-Salba-D3-AB6.trimmed.fastq
+cat l*R2_00*.trimmed.fastq > reverse-Salba-D3-AB6.trimmed.fastq
+cat l*.trimmed.single*.fastq > single-Salba-D3-AB6.trimmed.fastq
+

diff --git a/Personnel/albader/fastq_to_fasta.sh b/Personnel/albader/fastq_to_fasta.sh
new file mode 100755 (executable)
index 0000000..fd09027
--- /dev/null
+++ b/Personnel/albader/fastq_to_fasta.sh
@@ -0,0 +1,23 @@
+#!/bin/bash/
+#$ -cwd
+fastq_to_fasta -i lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R1_001.trimmed.fastq lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R1_001.trimmed.fasta
+fastq_to_fasta -i lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R1_002.trimmed.fastq lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R1_002.trimmed.fasta
+fastq_to_fasta -i lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R1_003.trimmed.fastq lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R1_003.trimmed.fasta
+fastq_to_fasta -i lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R2_001.trimmed.fastq lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R2_001.trimmed.fasta
+fastq_to_fasta -i lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R2_002.trimmed.fastq lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R2_002.trimmed.fasta
+fastq_to_fasta -i lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R2_003.trimmed.fastq lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_R2_003.trimmed.fasta
+fastq_to_fasta -i lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_trimmed_single.fastq lane4-index08-ACTTGA-Salba-D3-AB6-R1_ACTTGA_L004_trimmed_single.fasta
+fastq_to_fasta -i lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R1_001.trimmed.fastq lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R1_001.trimmed.fasta
+fastq_to_fasta -i lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R1_002.trimmed.fastq lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R1_002.trimmed.fasta
+fastq_to_fasta -i lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R1_003.trimmed.fastq lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R1_003.trimmed.fasta
+fastq_to_fasta -i lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R2_001.trimmed.fastq lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R2_001.trimmed.fasta
+fastq_to_fasta -i lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R2_002.trimmed.fastq lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R2_002.trimmed.fasta
+fastq_to_fasta -i lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R2_003.trimmed.fastq lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_R2_003.trimmed.fasta
+fastq_to_fasta -i lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_trimmed_single.fastq lane4-index16-CCGTCC-Salba-D3-AB6-R2_CCGTCC_L004_trimmed_single.fasta
+fastq_to_fasta -i lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_001.trimmed.fastq lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_001.trimmed.fasta
+fastq_to_fasta -i lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_002.trimmed.fastq lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_002.trimmed.fasta
+fastq_to_fasta -i lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_003.trimmed.fastq lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R1_003.trimmed.fasta
+fastq_to_fasta -i lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R2_001.trimmed.fastq lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R2_001.trimmed.fasta
+fastq_to_fasta -i lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R2_002.trimmed.fastq lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R2_002.trimmed.fasta
+fastq_to_fasta -i lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R2_003.trimmed.fastq lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_R2_003.trimmed.fasta
+fastq_to_fasta -i lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_trimmed_single.fastq lane4-index24-GGTAGC-Salba-D3-AB6-R3_GGTAGC_L004_trimmed_single.fasta