Question: Converting To Index Files Of Viral Genome For Running Tophat
gravatar for shamsher jagat
6.4 years ago by
United States
shamsher jagat590 wrote:
I was wondering if it is some how possible in galaxy to format FAST genome seq file of microbial genome to format to generate bowtie index so that it can be used for RNA seq analysis using TopHat. Alternatively any pointer to an available tool which can generate index files. Thanks Kanwar
alignment bowtie • 1.0k views
ADD COMMENTlink modified 6.4 years ago by Jennifer Hillman Jackson25k • written 6.4 years ago by shamsher jagat590
gravatar for Jennifer Hillman Jackson
6.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Kanwar, If you want to use a microbial genome, it can be used as a custom reference genome in Galaxy the same as any other reference genome, with Bowtie or TopHat. Instructions are at this wiki: To index the data and use in a local instance, you will want to create the indexes on the command line. Follow the instructions in our admin wiki: The above are technical set-up. There are still scientific considerations. Reviewing the RNA-seq pipeline's manuals, researching Q/A on message boards such as, and perhaps contacting the tool authors would be strongly recommended to determine if this is the appropriate tool set for your purposes: Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 6.4 years ago by Jennifer Hillman Jackson25k
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