Hi Zain,

I believe we already worked out the .fastqsanger/grooming part of this question in another thread. But for others reading this post, this is a help link:
See "FASTQ"
http://wiki.galaxyproject.org/Support#Dataset_special_cases

Our RNA-exercise covers and example workflow:
https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

Best,

Jen
Galaxy team

On 5/3/13 8:59 PM, Zain A Alvi wrote:
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.

Sincerely,

Zain 


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