how to look for known fusion in fastq file

[angerusso]

Hello:

I have an internal data for NCI-h660 file with 8m mapped pairs (HiSeq, 50bp paired end data) and I have an external dataset (4m mapped pairs, 50 bp paired end generated on GAII).

Questions:
1. I observe TMPRSS2-ERG fusion with external dataset, not with internal data from HiSeq. What could be the reasons? I use tophat2 fusion with same parameters for both the datasets.

2. How can I investigate the FASTQ file to see if this fusion is present. The sequence of ERG-TMPRSS2 fusion is as mentioned here:

http://info.gersteinlab.org/images/c/cc/FusionSeq_results.jpg

3. Does this mean we need more data generated internally to find the same fusion?
I use the following possible thresholds that are the minimum possible:

tophat-fusion-post -p $np --skip-read-dist --num-fusion-reads 1 --num-fusion-pairs 1 --num-fusion-both 2 $index

Any help will be greatly appreciated!! Thanks.

[GenoMax]

You have 2x the reads in internal dataset yet can't find the fusion (how many reads are supporting that observation in the external dataset?). Have you considered the possibility that one of these two data sets may be not what they are supposed to be?