Commit c1339ac1 authored by Noort, Maite van den's avatar Noort, Maite van den
Browse files

Update commands_methylation.sh

parent 08995151
# In this file are all the commands used for the step methylation in the material en methodes of the report.
# 1.
#This ensures that there is a link to the output_demulitplex directory of the original library 1 output
ln -s "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane2/output_demultiplex/" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/lane2_denovo8/epigbs2/output/"
# 2.
#This ensures that there is a link to the output_demulitplex directory of the original library 2 output
ln -s "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane8/output_demultiplex/" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/lane8_thenovo2/epiGBS2/Output_lane8_thenovo2/"
# 3.
#This ensures that there is a link to the file with de novo of library 1
ln -s "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane2/output_denovo/consensus_cluster.renamed.fa" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/lane2_denovo8/epigbs2/output/output_denovo/"
# 4.
#This ensures that there is a link to the file with de novo of library 2
ln -s "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane8/output_denovo/consensus_cluster.renamed.fa" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/lane8_thenovo2/epiGBS2/Output_lane8_thenovo2/output_denovo/"
# 5.
#This ensures that there is a link to the unassembled R1 reads from library 1
ln -s "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane2/output_demultiplex/Unassembled.R1.watson.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/lane2_denovo8/epigbs2/output/output_denovo/"
# 6.
#This ensures that there is a link to the unassembled R2 reads from library 1
ln -s "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane2/output_demultiplex/Unassembled.R2.crick.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/lane2_denovo8/epigbs2/output/output_denovo/"
# 7.
#This ensures that there is a link to the assembled reads from library 1
ln -s "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane2/output_demultiplex/Assembled.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/lane2_denovo8/epigbs2/output/output_denovo/"
# 8.
#This ensures that there is a link to the unassembled R1 reads from library 2
ln -s "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane8/output_demultiplex/Unassembled.R1.watson.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/lane8_thenovo2/epiGBS2/Output_lane8_thenovo2/output_denovo/"
# 9.
#This ensures that there is a link to the unassembled R2 reads from library 2
ln -s "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane8/output_demultiplex/Unassembled.R2.crick.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/lane8_thenovo2/epiGBS2/Output_lane8_thenovo2/output_denovo/"
# 10.
#This ensures that there is a link to the assembled reads from library 2
ln -s "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/output_lane8/output_demultiplex/Assembled.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/lane8_thenovo2/epiGBS2/Output_lane8_thenovo2/output_denovo/"
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