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command <<< |
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command <<< |
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set -o pipefail |
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set -o pipefail |
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set -e |
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set -e |
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echo 1 > /proc/sys/vm/overcommit_memory |
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mkdir -p ${sample_id}/spladder_out/spladder |
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mkdir -p ${sample_id}/spladder_out/spladder |
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ln -s ${bam}/*.bam ./ |
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ln -s ${bam}/*.bam ./ |
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--merge-strat merge_graphs \ |
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--merge-strat merge_graphs \ |
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--readlen 150 \ |
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--readlen 150 \ |
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--parallel $nt \ |
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--parallel $nt \ |
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--event-types exon_skip |
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--event-types exon_skip,intron_retention,alt_3prime,alt_5prime,mutex_exons,mult_exon_skip |
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find . -depth > fileList.txt |
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find . -depth > fileList.txt |
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>>> |
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>>> |