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
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