Commit 978198e9 authored by Noort, Maite van den's avatar Noort, Maite van den
Browse files

Add commands_bigdenovo.sh

parent 27a30b07
#merging the Watson_R1.fq.gz file from de demultiplexed reads from library 1 and library 2. This results in one Watson_R1.fq.gz file in the output #directory output_demultiplex from the big de novo.
Cat "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane2/output_demultiplex/Watson_R1.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane8/output_demultiplex/Watson_R1.fq.gz" > "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/big_de_novo/output_big_denovo/output_demultiplex/Watson_R1.fq.gz"
#merging the Watson_R2.fq.gz file from de demultiplexed reads from library 1 and library 2. This results in one Watson_R2.fq.gz file in the output #directory output_demultiplex from the big de novo.
Cat "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane2/output_demultiplex/Watson_R2.fq.gz " "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane8/output_demultiplex/Watson_R2.fq.gz " > "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/big_de_novo/output_big_denovo/output_demultiplex/Watson_R2.fq.gz "
#merging the Crick_R1.fq.gz file from de demultiplexed reads from library 1 and library 2. This results in one Crick_R1.fq.gz file in the output #directory output_demultiplex from the big de novo.
Cat "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane2/output_demultiplex/Crick_R1.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane8/output_demultiplex/Crick_R1.fq.gz" > "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/big_de_novo/output_big_denovo/output_demultiplex/Crick_R1.fq.gz"
#merging the Crick_R2.fq.gz file from de demultiplexed reads from library 1 and library 2. This results in one Crick_R2.fq.gz file in the output #directory output_demultiplex from the big de novo.
Cat "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane2/output_demultiplex/Crick_R2.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane8/output_demultiplex/Crick_R2.fq.gz" > "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/big_de_novo/output_big_denovo/output_demultiplex/Crick_R2.fq.gz"
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