My name is Ying, a postdotoral associate working in Yale university. I am trying
to use tophat in galaxy to analyze paired-end RNA-seq data, however, after I
groomer and use tophat to analyze them, I only got an empty file. I am
wondering what is the problem here. One thing I am concerned is that my files
is kind of large, e.g., for each end I got a file with 20.7 gb, so totally 41.4
gb for both ends of this sample. So do you think it is because the files are too
big? Also when the genome center sent me the data, they already separate the two
ends into two files, so I uploaded two files for one sample, but when do tophat
analysis, do I need to merge those two files into one file? do you know what is
the usual parameter set up for paried-end RNA-seq analysis(with a 300 bp
fragment)? Thank you very much! I really appreciate your help!


Ying Zhang, M.D., Ph.D.
Postdoctoral Associate
Department of Genetics,
Yale University School of Medicine
300 Cedar Street,S320
New Haven, CT 06519
Tel: (203)737-2616
Fax: (203)737-2286
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