I missed 2 BT474 and SKBR3 fusions using tophat2. I think I was supposed to find 25/27 of these fusions according to tophat paper. Can anyone help me with why could this be? See below my parameters:

BT474 CPNE1-PI3

BT474 LAMP1-MCF2L

SKBR3 CCDC85C-SETD3

SKBR3 CSE1L-ENSG00000236127

SKBR3 WDR67-ZNF704

> tophat2 -o $file -r 24 -p $np --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search --mate-std-dev 80 --max-intron-length 100000 --fusion-min-dist 100000 --fusion-anchor-length 13 --segment-mismatches 2 --segment-length 25 --fusion-ignore-chromosomes chrM $index $read1 $read2

> tophat-fusion-post -p $np --num-fusion-reads 1 --num-fusion-pairs 1 --num-fusion-both 2 $index

BT474 CPNE1-PI3

BT474 LAMP1-MCF2L

SKBR3 CCDC85C-SETD3

SKBR3 CSE1L-ENSG00000236127

SKBR3 WDR67-ZNF704

> tophat2 -o $file -r 24 -p $np --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search --mate-std-dev 80 --max-intron-length 100000 --fusion-min-dist 100000 --fusion-anchor-length 13 --segment-mismatches 2 --segment-length 25 --fusion-ignore-chromosomes chrM $index $read1 $read2

> tophat-fusion-post -p $np --num-fusion-reads 1 --num-fusion-pairs 1 --num-fusion-both 2 $index

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