Commit 25c7332e authored by Kosmas Hench's avatar Kosmas Hench

include data output

parent 84816a28
......@@ -11,7 +11,7 @@ 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
bowtie2-build HP_genome_unmasked_01.fa bt_db/bt_HPref
mkdir -p $WORK/1-output/10_recLandscape
cd $WORK/1-output/10_recLandscape
......@@ -25,3 +25,7 @@ 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
# extract mapping positions
awk '{print $1"\t"$3"\t"$4}' RADtags_map1.ref.sam > MAP1Mb.txt
awk '{print $1"\t"$3"\t"$4}' RADtags_map2.ref.sam > MAP2Mb.txt
\ No newline at end of file
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