1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
|
#!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
CPU=$(nproc || sysctl -n hw.physicalcpu)
../../Trinity --seqType fq --max_memory 2G \
--left reads.left.fq \
--right reads.right.fq \
--SS_lib_type RF \
--CPU ${CPU} \
--output trinity_with_workdir \
--workdir /tmp/trinity.workdir.$$ --full_cleanup
|