What is the best way to obtain the reads/read pairs mapping across fusion junctions?
Does the pseudobam file from kallisto indicate alignment of mate to another transcript in the same way as the standard bam format? Does it report supplementary/secondary alignments for split reads?
What is the best way to obtain the reads/read pairs mapping across fusion junctions? Does the pseudobam file from kallisto indicate alignment of mate to another transcript in the same way as the standard bam format? Does it report supplementary/secondary alignments for split reads?