Question: tophat-fusion for gene fusion detection
gravatar for Jackie
2.3 years ago by
United States
Jackie40 wrote:

I am trying to use tophat-fusion for gene fusion detection. 

my data (fastq files) are paired-end, and I have fastq files from multiple lanes, and they are compressed. (fastq.gz).

I am wondering (1) if tophat can take fastq files from multiple lanes in one command line as STAR can; (2) can tophat take fastq.gz files?

Because of the size of the data, it's difficult for me to unzip the fastq files, and merge the ones from multiple lanes into one, it will be not efficient.

Thanks for your help!










rna-seq sequence alignment • 1.2k views
ADD COMMENTlink written 2.3 years ago by Jackie40

Also, the same questions for deFuse. I want to compare the results from multiple tools.

ADD REPLYlink written 2.3 years ago by Jackie40

If I remember right gene fusion finder SOAPfuse and FusionCatcher will do that automatically for you!

ADD REPLYlink written 2.3 years ago by enxxx23160
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