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DROP seq
Hyunmin Kim edited this page Jun 20, 2021
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Drop-seq pipelines:
https://github.com/broadinstitute/Drop-seq/blob/master/doc/Drop-seq_Alignment_Cookbook.pdf
## file : TagBamWithReadSequenceExtended
## switch UseParallelOldGC with UseG1GC if not working
#java -Xmx${xmx} -XX:+UseParallelOldGC -XX:ParallelGCThreads=1 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+HeapDumpOnOutOfMemoryError -Djava.io.tmpdir=$TMPDIR -jar $jar_deploy_dir/dropseq.jar $progname $*
java -Xmx${xmx} -XX:+UseG1GC -XX:ParallelGCThreads=1 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+HeapDumpOnOutOfMemoryError -Djava.io.tmpdir=$TMPDIR -jar $jar_deploy_dir/dropseq.jar $progname $*