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3_Assembly analysis
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3_Assembly analysis
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-------------------------------------------------------------------------------------------------------
#Assembly Analysis, BUSCO and TransRate
#Hippocampus
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies/tuco_hippocampus.assembly.trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_hippocampus.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_hippocampus.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_hippocampus
TRANSRATEOUT :=TRANSRATE_hippocampus
all:/data/andrew/analysis/run_BUSCO_hippocampus /data/andrew/analysis/TRANSRATE_hippocampus
/data/andrew/analysis/run_BUSCO_hippocampus:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_hippocampus:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Hypothalamus
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies/tuco_hypothalamus.assembly.trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_hypothalamus.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_hypothalamus.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_hypothalamus
TRANSRATEOUT :=TRANSRATE_hypothalamus
all:/data/andrew/analysis/run_BUSCO_hypothalamus /data/andrew/analysis/TRANSRATE_hypothalamus
/data/andrew/analysis/run_BUSCO_hypothalamus:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_hypothalamus:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Kidney
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies/tuco_kidney.assembly.trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_kidney.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_kidney.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_kidney
TRANSRATEOUT :=TRANSRATE_kidney
all:/data/andrew/analysis/run_BUSCO_kidney /data/andrew/analysis/TRANSRATE_kidney
/data/andrew/analysis/run_BUSCO_kidney:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_kidney:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Liver
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies/tuco_liver.assembly.trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_liver.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_liver.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_liver
TRANSRATEOUT :=TRANSRATE_liver
all:/data/andrew/analysis/run_BUSCO_liver /data/andrew/analysis/TRANSRATE_liver
/data/andrew/analysis/run_BUSCO_liver:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_liver:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Ovary
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies/tuco_ovary.assembly.trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_ovary.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_ovary.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_ovary
TRANSRATEOUT :=TRANSRATE_ovary
all:/data/andrew/analysis/run_BUSCO_ovary /data/andrew/analysis/TRANSRATE_ovary
/data/andrew/analysis/run_BUSCO_ovary:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_ovary:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Skin
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies/tuco_skin.assembly.trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_skin.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_skin.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_skin
TRANSRATEOUT :=TRANSRATE_skin
all:/data/andrew/analysis/run_BUSCO_skin /data/andrew/analysis/TRANSRATE_skin
/data/andrew/analysis/run_BUSCO_skin:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_skin:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Spleen
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies/tuco_spleen.assembly.trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_spleen.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_spleen.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_spleen
TRANSRATEOUT :=TRANSRATE_spleen
all:/data/andrew/analysis/run_BUSCO_spleen /data/andrew/analysis/TRANSRATE_spleen
/data/andrew/analysis/run_BUSCO_spleen:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_spleen:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Testes
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies/tuco_testes.assembly.trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_testes.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_testes.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_testes
TRANSRATEOUT :=TRANSRATE_testes
all:/data/andrew/analysis/run_BUSCO_testes /data/andrew/analysis/TRANSRATE_testes
/data/andrew/analysis/run_BUSCO_testes:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_testes:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
-------------------------------------------------------------------------------------------------------
#Normalized Assembly Analysis, BUSCO and TransRate
#Hippocampus_norm.mk
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies_norm/tuco_hippocampus.norm_trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_hippocampus.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_hippocampus.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_hippocampus.norm
TRANSRATEOUT :=TRANSRATE_hippocampus.norm
all:/data/andrew/analysis/run_BUSCO_hippocampus.norm /data/andrew/analysis/TRANSRATE_hippocampus.norm
/data/andrew/analysis/run_BUSCO_hippocampus.norm:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_hippocampus.norm:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Hypothalamus_norm.mk
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies_norm/tuco_hypothalamus.norm_trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_hypothalamus.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_hypothalamus.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_hypothalamus.norm
TRANSRATEOUT :=TRANSRATE_hypothalamus.norm
all:/data/andrew/analysis/run_BUSCO_hypothalamus.norm /data/andrew/analysis/TRANSRATE_hypothalamus.norm
/data/andrew/analysis/run_BUSCO_hypothalamus.norm:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_hypothalamus.norm:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Kidney_norm.mk
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies_norm/tuco_kidney.norm_trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_kidney.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_kidney.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_kidney.norm
TRANSRATEOUT :=TRANSRATE_kidney.norm
all:/data/andrew/analysis/run_BUSCO_kidney.norm /data/andrew/analysis/TRANSRATE_kidney.norm
/data/andrew/analysis/run_BUSCO_kidney.norm:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_kidney.norm:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Liver_norm.mk
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies_norm/tuco_liver.norm_trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_liver.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_liver.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_liver.norm
TRANSRATEOUT :=TRANSRATE_liver.norm
all:/data/andrew/analysis/run_BUSCO_liver.norm /data/andrew/analysis/TRANSRATE_liver.norm
/data/andrew/analysis/run_BUSCO_liver.norm:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_liver.norm:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Ovary_norm.mk
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies_norm/tuco_ovary.norm_trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_ovary.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_ovary.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_ovary.norm
TRANSRATEOUT :=TRANSRATE_ovary.norm
all:/data/andrew/analysis/run_BUSCO_ovary.norm /data/andrew/analysis/TRANSRATE_ovary.norm
/data/andrew/analysis/run_BUSCO_ovary.norm:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_ovary.norm:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Skin_norm.mk
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies_norm/tuco_skin.norm_trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_skin.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_skin.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_skin.norm
TRANSRATEOUT :=TRANSRATE_skin.norm
all:/data/andrew/analysis/run_BUSCO_skin.norm /data/andrew/analysis/TRANSRATE_skin.norm
/data/andrew/analysis/run_BUSCO_skin.norm:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_skin.norm:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
Spleen_norm.mk
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies_norm/tuco_spleen.norm_trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_spleen.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_spleen.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_spleen.norm
TRANSRATEOUT :=TRANSRATE_spleen.norm
all:/data/andrew/analysis/run_BUSCO_spleen.norm /data/andrew/analysis/TRANSRATE_spleen.norm
/data/andrew/analysis/run_BUSCO_spleen.norm:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_spleen.norm:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
#Testes_norm.mk
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/individual_assemblies_norm/tuco_testes.norm_trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_testes.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_testes.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_testes.norm
TRANSRATEOUT :=TRANSRATE_testes.norm
all:/data/andrew/analysis/run_BUSCO_testes.norm /data/andrew/analysis/TRANSRATE_testes.norm
/data/andrew/analysis/run_BUSCO_testes.norm:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_testes.norm:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
-------------------------------------------------------------------------------------------------------
#Compiled assembly analysis
SHELL=/bin/bash -o pipefail
MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
BUSCO ?= ${shell which BUSCO_v1.1b1.py}
BUSCODIR := $(dir $(firstword $(BUSCO)))
CPU=16
ASSEMBLY=/data/andrew/tuco_compiled_trinity.Trinity.fasta
READ1=/data/andrew/reads_corrected/tuco_hippocampus.1.cor.fq,/data/andrew/reads_corrected/tuco_hypothalamus.1.cor.fq,/data/andrew/reads_corrected/tuco_kidney.1.cor.fq,/data/andrew/reads_corrected/tuco_liver.1.cor.fq,/data/andrew/reads_corrected/tuco_ovary.1.cor.fq,/data/andrew/reads_corrected/tuco_skin.1.cor.fq,/data/andrew/reads_corrected/tuco_spleen.1.cor.fq,/data/andrew/reads_corrected/tuco_testes.1.cor.fq
READ2=/data/andrew/reads_corrected/tuco_hippocampus.2.cor.fq,/data/andrew/reads_corrected/tuco_hypothalamus.2.cor.fq,/data/andrew/reads_corrected/tuco_kidney.2.cor.fq,/data/andrew/reads_corrected/tuco_liver.2.cor.fq,/data/andrew/reads_corrected/tuco_ovary.2.cor.fq,/data/andrew/reads_corrected/tuco_skin.2.cor.fq,/data/andrew/reads_corrected/tuco_spleen.2.cor.fq,/data/andrew/reads_corrected/tuco_testes.2.cor.fq
LINEAGE=vertebrata
BUSCOUT :=BUSCO_tuco_compiled
TRANSRATEOUT :=TRANSRATE_tuco_compiled
all:/data/andrew/analysis/run_BUSCO_tuco_compiled /data/andrew/analysis/TRANSRATE_tuco_compiled
/data/andrew/analysis/run_BUSCO_tuco_compiled:${ASSEMBLY}
python3 ${BUSCODIR}BUSCO_v1.1b1.py -in ${ASSEMBLY} -m trans --cpu $(CPU) -l ${BUSCODIR}${LINEAGE} -o ${BUSCOUT}
/data/andrew/analysis/TRANSRATE_tuco_compiled:${ASSEMBLY}
transrate -o ${TRANSRATEOUT} -a ${ASSEMBLY} --left ${READ1} --right ${READ2} -t $(CPU)
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#Run BUSCO on Transrate good.fasta individual assemblies to determine completeness
python3 /opt/BUSCO_v1.1b1/BUSCO_v1.1b1.py -in /data/andrew/analysis/TRANSRATE_hippocampus/tuco_hippocampus.assembly.trinity.Trinity/good.tuco_hippocampus.assembly.trinity.Trinity.fasta -m trans --cpu 16 -l /opt/BUSCO_v1.1b1/vertebrata -o BUSCO_hippocampus_good
python3 /opt/BUSCO_v1.1b1/BUSCO_v1.1b1.py -in /data/andrew/analysis/TRANSRATE_hypothalamus/tuco_hypothalamus.assembly.trinity.Trinity/good.tuco_hypothalamus.assembly.trinity.Trinity.fasta -m trans --cpu 16 -l /opt/BUSCO_v1.1b1/vertebrata -o BUSCO_hypothalamus_good
python3 /opt/BUSCO_v1.1b1/BUSCO_v1.1b1.py -in /data/andrew/analysis/TRANSRATE_kidney/tuco_kidney.assembly.trinity.Trinity/good.tuco_kidney.assembly.trinity.Trinity.fasta -m trans --cpu 16 -l /opt/BUSCO_v1.1b1/vertebrata -o BUSCO_kidney_good
python3 /opt/BUSCO_v1.1b1/BUSCO_v1.1b1.py -in /data/andrew/analysis/TRANSRATE_liver/tuco_liver.assembly.trinity.Trinity/good.tuco_liver.assembly.trinity.Trinity.fasta -m trans --cpu 16 -l /opt/BUSCO_v1.1b1/vertebrata -o BUSCO_liver_good
python3 /opt/BUSCO_v1.1b1/BUSCO_v1.1b1.py -in /data/andrew/analysis/TRANSRATE_ovary/tuco_ovary.assembly.trinity.Trinity/good.tuco_ovary.assembly.trinity.Trinity.fasta -m trans --cpu 16 -l /opt/BUSCO_v1.1b1/vertebrata -o BUSCO_ovary_good
python3 /opt/BUSCO_v1.1b1/BUSCO_v1.1b1.py -in /data/andrew/analysis/TRANSRATE_skin/tuco_skin.assembly.trinity.Trinity/good.tuco_skin.assembly.trinity.Trinity.fasta -m trans --cpu 16 -l /opt/BUSCO_v1.1b1/vertebrata -o BUSCO_skin_good
python3 /opt/BUSCO_v1.1b1/BUSCO_v1.1b1.py -in /data/andrew/analysis/TRANSRATE_spleen/tuco_spleen.assembly.trinity.Trinity/good.tuco_spleen.assembly.trinity.Trinity.fasta -m trans --cpu 16 -l /opt/BUSCO_v1.1b1/vertebrata -o BUSCO_spleen_good
python3 /opt/BUSCO_v1.1b1/BUSCO_v1.1b1.py -in /data/andrew/analysis/TRANSRATE_testes/tuco_testes.assembly.trinity.Trinity/good.tuco_testes.assembly.trinity.Trinity.fasta -m trans --cpu 16 -l /opt/BUSCO_v1.1b1/vertebrata -o BUSCO_testes_good
python3 /opt/BUSCO_v1.1b1/BUSCO_v1.1b1.py -in /data/andrew/TRANSRATE_tuco_compiled/tuco_compiled_trinity.Trinity/good.tuco_compiled_trinity.Trinity.fasta -m trans --cpu 16 -l /opt/BUSCO_v1.1b1/vertebrata -o BUSCO_tuco_compiled_good