Using Tophat-Fusion to detect Structural Variation in E. coli

[aaronreba]

Hello,

I'm trying to use Tophat-Fusion on a set of E. coli for structural variation detection. The program seems to run with no errors, but the output doesn't seem correct.

I have a few simple questions first.

When giving paired end reads to Tophat-Fusion, how should they be passed? Should they be in separate files with similar names like set_of_reads_1.fastq and set_of_reads_2.fastq with corresponding read names for the pairs? Or should they be merged into one file like set_of_reads.fastq such that as the file is being read, every 2 reads is a pair?

I have built my bowtie files like so:
bowtie-build REL606.5.gbk bowtie_REL606.5
Which seems to build correctly.

My reads are 50 bps in length with a gap size of 100. I then call tophat like so:

tophat-fusion -p 12 --solexa-quals -r 100 --mate-std-dev 20 -o paired_tophat bowtie_REL606.5 set_1.fastq set_2.fastq

tophat-fusion -p 12 --solexa-quals -r 100 --mate-std-dev 20 -o merged_tophat bowtie_REL606.5 set.fastq

I have called it in 2 different ways because I'm unsure of the read method I mentioned above.

When it completed, I tried examining the sam file but the samtools view command fails with the following error:
[sam_read1] reference 'REL606.5-REL606.5' is recognized as '*'.
Parse error at line 2428: invalid CIGAR operation

How would I be able to examine the sam file?

Platform: Linux

Versions:
TopHat v0.1.0 (Beta)
bowtie version 0.12.7
Samtools Version: 0.1.15 (r949:203)

Thanks

[aaronreba]

I've found out my questions for anyone else interested. I was apparently using an old version of Tophat. I learned this after downloading only the binaries of Tophat2. The reads also must be in separate files like so:

File 1:

read1.1
atgatgc...
+
#$@#$...
read2.1
atgatgc...
+
#$@#$...

File 2:

read1.2
atgatgc...
+
#$@#$...
read2.2
atgatgc...
+
#$@#$...