Dear Sir or Madam,

I hope this reaches you well. Lately, I have been trying to use tophat and then 
use bowtie on Galaxy project to create an aligned BAM file. The original data 
came from a SRA file that I have acquired from the Japanese DNA Databank. This 
SRA was then converted to FASTQ using the tools available on Galaxy project. 
Now when I go under Tophat on Galaxy Project, I am unable to select the 
converted RNA-Seq FASTQ file. I was wondering, is there a specific format for 
the file to be in. Currently it is just a *.fastq file.  I am confused as to 
why I am not being able to select the FASTQ file.

Also if there is a guide on how to use Galaxy Project to create an aligned BAM 
file and then check for expression through Cufflinks package. I would really 
appreciate it.


Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

To search Galaxy mailing lists use the unified search at:

Reply via email to