REF_FILE_NAME a_thaliana.gtf READ_NUMBER 8000000 GEN_DIR FASTA_REF TMP_DIR /s/eggs/a/tmp/rogersma/at_full RT_MIN 400 RT_MAX 2600 RT_PRIMER RH LOAD_NONCODING FALSE POLYA_SHAPE Nan POLYA_SCALE Nan FRAG_METHOD UR FRAG_SUBSTRATE RNA FILTERING YES READ_LENGTH 100 PAIRED_END TRUE FASTA TRUE ERR_FILE 76