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David Ray
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corrected missing &&
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template_rm2bed.sh

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@@ -33,7 +33,7 @@ DIR=DIRPATH/$RUNTYPE
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cd $DIR
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#Runs a python script RM2bed to generate one complete .bed file and several subfiles subdivided by TE class. Merges overlapping hits based using 'lower_divergence' criterion.
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[ ! -f ${GENOME}_rm.bed ] python /home/daray/gitrepositories/bioinfo_tools/RM2bed.py -d . -sp class -p ${GENOME} -o lower_divergence ${GENOME}.fa.align.gz
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[ ! -f ${GENOME}_rm.bed ] && python /home/daray/gitrepositories/bioinfo_tools/RM2bed.py -d . -sp class -p ${GENOME} -o lower_divergence ${GENOME}.fa.align.gz
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#Calculate genome size by counting all characters in .masked.fa.gz file that are not on a line begining with >. Assign the value to GENOMESIZE.
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echo "calculating genome size"

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