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
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org