#SAMTOOLS_GENOME /lustre/isilon/Mondas_software/Genomes/HumanNCBI36Fasta_all/all/HumanNCBI36Fasta_all.fa
ELAND_GENOME /lustre/isilon/Mondas_software/Genomes/HumanNCBI36Fasta_all
ELAND_SET_SIZE 2
4:ANALYSIS eland_pair
4:USE_BASES Y45n,I9,y45n
#2:ANALYSIS eland_rna
#2:USE_BASES Y35n*,n*
#3:ANALYSIS eland_extended
#3:USE_BASES n*,Y35n*
#4:ANALYSIS sequence
#4:USE_BASES Y35n*,n*
1235678:ANALYSIS none
ELAND_RNA_GENOME_SEQ_GENE_MD_GZ /home/rpetrovski/CASAVA_INSTALL/BF00806/CASAVA_BF00808_fddt01/share/CASAVA-1.8.0BF00806_101007/examples/features/human/NCBI/Build36.3/seq_gene.md.gz
ELAND_RNA_GENOME_CONTAM /home/craczy/validation-1.7/Genomes
#CHROM_NAME_VALIDATION off
#INPUT_FORMAT qseq