Commit 84816a28 authored by Kosmas Hench's avatar Kosmas Hench

include 1.2.9.remapRADtags script

parent bad3f5b1
......@@ -9,6 +9,7 @@
# build bowtie index for gap-closed assembly
cd $WORK/1-output/05_PBjelly
mkdir -p bt_db
bowtie2-build jelly.out.fasta bt_db/bt_jelly
# unpack RADtags for mapping
......
......@@ -2,7 +2,7 @@
#PBS -l memsz_job=30gb
#PBS -b 1
#PBS -l cpunum_job=1
#PBS -N manual
#PBS -N hp2ga
#PBS -q clmedium
#PBS -o 1.2.8.align2GA.stdout
#PBS -e 1.2.8.align2GA.stderr
......@@ -15,7 +15,7 @@ lastdb -uNEAR -cR11 HPdb HP_genome_unmasked_01.fa
cd $WORK/1-output/08_Synteny
# download the Stickleback reference genome from Roesti et al 2014
wget https://datadryad.org/bitstream/handle/10255/dryad.58821/G.ac_2006_corrected_v2.fa?sequence=2
mv ./G.ac_2006_corrected_v2.fa\?sequence\=2 G.ac_2006_corrected_v2.fa
mv ./G.ac_2006_corrected_v2.fa\?sequence\=2 G.ac_2006_corrected_v2.fa
# align Stickleback reference genome with assembly
lastal -m50 -E0.05 $WORK/1-output/07_final_assembly/HPdb G.ac_2006_corrected_v2.fa | last-split -m1 > synteny.maf
#PBS -l elapstim_req=01:00:00
#PBS -l memsz_job=6gb
#PBS -b 1
#PBS -l cpunum_job=1
#PBS -N remap
#PBS -q clexpress
#PBS -o 1.2.9.remapRADtags.stdout
#PBS -e 1.2.9.remapRADtags.stderr
cd $WORK/1-output/07_final_assembly/
# build bowtie index for anchored assembly
mkdir -p bt_db
bowtie2-build jelly.out.fasta bt_db/bt_HPref
mkdir -p $WORK/1-output/10_recLandscape
cd $WORK/1-output/10_recLandscape
# map RAD tags of map1 & map2
bowtie2 --no-head --no-unal -a \
-x ../07_final_assembly/bt_db/bt_HPref \
-f $WORK/0_data/0_resources/map_1_RADtags.fa \
-S RADtags_map1.ref.sam
bowtie2 --no-head --no-unal -a \
-x ../07_final_assembly/bt_db/bt_HPref \
-f $WORK/0_data/0_resources/map_2_RADtags.fa \
-S RADtags_map2.ref.sam
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