Tophat for multiple files.

[oxydeepu]

Hi all,

I have three fastq file for a sample. two paired end reads and a single - end read for the same.
I want to run tophat for all together. i want to know is it possible to run 3 fq files with tophat.
Or can you please suggest a way of doing it..??

Thanking you in advance
Deepak

[westerman]

About the 15th line of the manual.

Finally, mixing paired- and single- end reads together is not supported.

And about the 60th line in the manual:

tophat [options]* <index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]

So the answer to your question is "no" and "yes".

Read the manual. It may help.