Commit 08995151 authored by Noort, Maite van den's avatar Noort, Maite van den
Browse files

Update commands_aligning_reads_bigdenovo.sh

parent 4e42d4c6
......@@ -8,18 +8,18 @@ Ln -s "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/big_de_no
#This ensures that there is a link to the created big de novo reference file to lib2
Ln -s "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/big_de_novo/output_big_denovo/output_denovo/consensus_cluster.renamed.fa" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/library2/outputlib2/output_denovo/"
#This ensures that there is a link to the unassembled R1 reads from library 1
#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_denovo/Unassembled.R1.watson.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/library1/output_lib1/output_denovo/"
#This ensures that there is a link to the unassembled R2 reads from library 1
#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_denovo/Unassembled.R2.crick.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/library1/output_lib1/output_denovo/"
#This ensures that there is a link to the assembled reads from library 1
#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_denovo/Assembled.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/library1/output_lib1/output_denovo/"
#This ensures that there is a link to the unassembled R1 reads from library 2
#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_lane2/output_denovo/Unassembled.R1.watson.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/library2/outputlib2/output_denovo/"
#This ensures that there is a link to the unassembled R2 reads from library 2
#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_lane2/output_denovo/Unassembled.R2.crick.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/library2/outputlib2/output_denovo/"
#This ensures that there is a link to the assembled reads from library 2
#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_lane2/output_denovo/Assembled.fq.gz" "/mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/big_denono/library2/outputlib2/output_denovo/"
......
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