the description in the online manual for cufflinks describes -j as:
"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 5%. "
So for a set of 100 split alignments, 90 split alignments define the same exon-exon boundary. 10 crosses into the intron and the overlaps form a minimum coverage depth of 1 at a certain base pair within the intronic region. So in this case, under default setting of 5%, cufflinks will calculate the 'j' value as 1/100 and discard it?
When calculating the minimum depth coverage in the intron, is it only using split alignment that cross into the intron? Or is it looking at all mapped alignments (split or complete)?
If it is looking at all alignments that covers the intronic region to determine the minimum coverage depth, isn't it possible that the 'j' value be greater than 1?
"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 5%. "
So for a set of 100 split alignments, 90 split alignments define the same exon-exon boundary. 10 crosses into the intron and the overlaps form a minimum coverage depth of 1 at a certain base pair within the intronic region. So in this case, under default setting of 5%, cufflinks will calculate the 'j' value as 1/100 and discard it?
When calculating the minimum depth coverage in the intron, is it only using split alignment that cross into the intron? Or is it looking at all mapped alignments (split or complete)?
If it is looking at all alignments that covers the intronic region to determine the minimum coverage depth, isn't it possible that the 'j' value be greater than 1?
