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#sample replicate left.reads right.reads
heatshock hs_rep1 ../test_DATA/Sp_hs.10k.left.fq.gz ../test_DATA/Sp_hs.10k.right.fq.gz
plateau plat_rep1 ../test_DATA/Sp_plat.10k.right.fq.gz ../test_DATA/Sp_plat.10k.left.fq.gz
log_growth log_rep1 ../test_DATA/Sp_log.10k.left.fq.gz ../test_DATA/Sp_log.10k.right.fq.gz
diauxic_shift ds_rep1 ../test_DATA/Sp_ds.10k.right.fq.gz ../test_DATA/Sp_ds.10k.left.fq.gz
## Trinity.pl configuration settings:
--CPU=4
--max_memory=1G
--seqType=fq
--SS_lib_type=RF
## analyze_diff_expr.pl settings
-P=0.1
-C=1
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