Minimum fraction of reads of a locus that must overlap with all CRL loci inorder to merge itinto that CRL.

Minimum number of reads a locus should have in order to participate in CRL creation. Always set this value relative to your sequencing depth. Setting this to lower leads CRLs of random multimappings Also consider setting the --crl_share option along with this

The maximum difference of transcripts expression between two consecutive iterations of EM algorithm to converge.

Create CRLs and qunatify them or use the loci further without creating the CRLs