tophat2 and cufflinks with and without --fusion-search

[angerusso]

Hello,

I have a question about using tophat2 with and without --fusion-search options for 5 cell lines of interest:

1. Is "accepted_hits.bam" file output the same with and without --fusion-search option? The reason I am asking is because I want to run cufflinks next using "accepted_hits.bam" as input and wondering which one I should use.

2. When I run tophat2 with --fusion-search option, I find deletion.bed and insertions.bed files are empty and just have one line as below. Why could this be?
track name=insertions description="TopHat insertions"
I understand INDELs are of no significance using RNASeq data. So does it matter if insertion/deletion files are empty?

Here's my ommand line:
> tophat2 -o $file -r 0 -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

Another question is how do I choose, "--fusion-anchor-length" and "segment length"?

2. Are these the next steps?
cufflinks -G genes.gtf -o sample1.bam
cufflinks -G genes.gtf -o sample2.bam

3. To use cuffcomapre:
cuffcompare -s hg19.fa -r genes.gtf Sample1_transcripts.gtf

I understand there's no need to run cuffdiff as I don't have any "normals" in case of cell lines to compare to. Am I correct?

Thanks very much.