Is there a size cutoff consideration for gaps in paired-end RNA-seq data in BAM format?
For instance, if the BAM file's CIGAR string is
50M422N26M, then is the read for regions across
26M supposed to be kept intact, because the value of
422N is too large? (Whereas, contrariwise, if the CIGAR string has a
N segment smaller than some value, then the read is indeed split across exon boundaries into two pieces?)
What other data in the BAM read would indicate that a split operation would not be appropriate, when an
N gap is listed in the CIGAR string?