Hello again,
The general path will be:
- "Convert Formats -> GFF-to-BED" - click on pencil icon to assign format as "interval", double checking the assignment of the columns, including strand.
From there you have different analysis choices, including:
* Find out which UCSC tracks have annotation for the gene regions themselves:
- "Operate on Genomic Intervals -> Profile Annotations"
* Find out which UCSC tracks have annotation for the upstream/downstream regions:
- "Operate on Genomic Intervals -> Get flanks" - "Operate on Genomic Intervals -> Profile Annotations"
* Extract sequence for the upstream/downstream regions:
- "Operate on Genomic Intervals -> Get flanks" - "Fetch Sequences -> Extract Genomic DNA"
* Extract complete annotation track from UCSC and find overlapping regions with your regions (any: genes or flanks)
- "Get Data -> UCSC Main" select your genome, track of interest (perhaps from profile annotations results, could limit by regions (UCSC accepts up to 1000 regions), etc. - "Operate on Genomic Intervals -> Coverage" this is one suggestion. See our wiki for other choices: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
Hopefully this helps to get you started,
Jen Galaxy team
On 4/4/12 9:01 AM, Abdullah Al Mahmud wrote:
Hi Jen,
Thank you for your reply. I uploaded a gff file to my galaxy. which contains almost 250 gene annotation. It is for D. melanogaster. I want to know using galaxy and UCSC genome browser is there a way to collect sequence information about 1000pb upstream and down stream of all the gene?
With best regards,
Abdullah
On Wed, Apr 4, 2012 at 10:59 AM, Jennifer Jacksonjen@bx.psu.edu wrote:
Hello Abdullah,
Galaxy can convert BED data to GFF data (type in "GFF" in tool search, top of right tool panel). So, any BED file created (MACS, etc.) or imported ("Get Data" or other) could be converted and exported as GFF. Please note this is "GFF", not "GFF3".
SeqMonk also accepts BED format, so converting may not be necessary. GTF and BAM/SAM are also accepted.
Is this what you wanted to know? Did you have a specific data in mind that you wanted to create/obtain for visualization?
Please let us know if we can help more,
Jen Galaxy team
On 4/2/12 12:18 PM, Abdullah Al Mahmud wrote:
Hi,
Is it possible to generate gff file in galaxy which I can use in Seqmonk?
Abdullah