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In advanced assembly options of cufflink, "--pre-mrna-fraction" tells us that "Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 15%.".
From some result using a real rna-seq dataset and different values of "--pre-mrna-fraction", I concluded that the value of ‘pre-mrna-fraction’ has little effect on known reference transcripts. But with bigger values of pre-mrna-fraction’, the number of novel isoforms (“j”) decreases.
My question is that why the value of ‘pre-mrna-fraction’ has little effect on known reference transcripts.
From some result using a real rna-seq dataset and different values of "--pre-mrna-fraction", I concluded that the value of ‘pre-mrna-fraction’ has little effect on known reference transcripts. But with bigger values of pre-mrna-fraction’, the number of novel isoforms (“j”) decreases.
My question is that why the value of ‘pre-mrna-fraction’ has little effect on known reference transcripts.