Jen, 

Thanks for all your help. 
Here's the final Galaxy workflow for doing FUZZNUC on a BED file from UCSC 
Table Browser, then producing BED file that you can view in UCSC. 

http://main.g2.bx.psu.edu/u/curtish-uab/w/fuzznucucscbed

I do not include the "Get Flank" operation in this base workflow, but include a 
note in the description. 
I have not (yet) had time to make the score in the final BED dependent on the 
quality of the match, when mis-matches are allowed, but I hope to come back and 
add that later. 

How does one handle versioning of published workflows? Do updated the existing 
one, or create another with a .v2 name? 

Also, I used several "Text Manipulation> Compute" steps - is there any way to 
compute more than 1 new column at a time? 


Regards, 
Curtis



> -----Original Message-----
> From: Jennifer Jackson [mailto:j...@bx.psu.edu]
> Sent: Wednesday, May 18, 2011 11:45 AM
> To: Robert Curtis Hendrickson
> Cc: galaxy-user
> Subject: Re: [galaxy-user] UCSC->EMBOSS/fuzznuc->UCSC workflow?
> 
> Hello Curtis,
> 
> The BED extraction data can be resolved in Galaxy. Pull out the whole
> gene and then modify the coordinates in Galaxy to be 10k upstream.
> 
> To be clear - this coordinate data is going to be used to transform the
> coordinates in your current fuzznuc output that is transcript-based to
> be genome-based. The coordinates are not input for fuzznuc - the are
> used after fuzznuc is run on the fasta file, in order to covert the
> result coordinates only.
> 
> This page in the UCSC wiki has a good description of how the UCSC
> coordinates are organized.
> http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms
> 
> The output format for fuzznuc is documented in the tool's help - the
> last line on the tool form has a link.
> 
> Hopefully this helps to clear up the suggested processing,
> 
> Thanks,
> 
> Jen
> Galaxy team
> 
> 
> 
> On 5/17/11 2:08 PM, Robert Curtis Hendrickson wrote:
> > Jennifer,
> >
> > I tried getting data from UCSC as .BED - two issues:
> >
> > 1. Unlike "get sequence", I can no longer specify how far upstream I
> > want - it's EITHER "whole gene" (what's the definition of that!!!) OR
> > #bp_upstream OR exons OR introns -- with get seq those are not mutually
> > exclusive - I happen to want the genomic region (5'UTR, exons, introns
> > 3'UTR + 10kbp upstream of 5'UTR)
> >
> > 2. fuzznuc does not recognize BED as a valid input format. So, I can't
> > run fuzznuc because my BED file doesn't' show up in the pulldown.
> >
> > Indeed, BED files are just annotation, they don't carry any sequence.
> >
> > Have I mis-understood your directions?
> >
> > Regards,
> >
> > Curtis
> >
> > -----Original Message-----
> > From: Jennifer Jackson [mailto:j...@bx.psu.edu]
> > Sent: Tuesday, May 17, 2011 11:23 AM
> > To: Robert Curtis Hendrickson
> > Cc: 'galaxy-user@lists.bx.psu.edu'
> > Subject: Re: [galaxy-user] UCSC->EMBOSS/fuzznuc->UCSC workflow?
> >
> > Hello Curtis,
> >
> > No need to use the fasta headers from your original fasta file.
> >
> > To obtain the coordinates in BED format: using "Get Data -> UCSC main"
> >
> > again to link to the UCSC Table browser, set the same selection criteria
> >
> > as for the original fasta sequence, only change the output type to be
> >
> > "BED" (instead of "sequence"). Once in your Galaxy history, this format
> >
> > will be easier to work with.
> >
> > Best,
> >
> > Jen
> >
> > Galaxy team
> >
> > On 5/16/11 9:04 PM, Robert Curtis Hendrickson wrote:
> >
> >  > Jennifer,
> >
> >  >
> >
> >  > Thanks for the outline. I'll try that approach.
> >
> >  >
> >
> >  > However, it seems rather painful to have to join the fuzznuc output
> > back to the original fasta to get at the header information that really
> > should have been passed along. It would see that there must be a way to
> > get the data out of UCSC without that space in the fasta header, so that
> > the chromosome& genomic location get correctly preserved in the fuzznuc
> > output. Failing that, is there an easy text manipulation that would
> > convert that fasta header space to a "|"?
> >
> >  >
> >
> >  > Regards,
> >
> >  > Curtis
> >
> >  >
> >
> >  >
> >
> >  > -----Original Message-----
> >
> >  > From: Jennifer Jackson [mailto:j...@bx.psu.edu]
> >
> >  > Sent: Monday, May 16, 2011 6:50 PM
> >
> >  > To: Robert Curtis Hendrickson
> >
> >  > Cc: 'galaxy-user@lists.bx.psu.edu'
> >
> >  > Subject: Re: [galaxy-user] UCSC->EMBOSS/fuzznuc->UCSC workflow?
> >
> >  >
> >
> >  > Hello Curtis,
> >
> >  >
> >
> >  > The coordinates of your match are with respect to the fasta sequence,
> >
> >  > not with respect to the reference genome. Only data mapped to the
> >
> >  > reference genome can be viewed in the UCSC Browser
> >
> >  >
> >
> >  > You will need to calculate from the position of the match in the fasta
> >
> >  > sequence back through to the reference genome.
> >
> >  >
> >
> >  > One suggested way to do this:
> >
> >  >
> >
> >  > a) Merge together the original genomic coordinates of the 2kb regions
> >
> >  > with each line of output from fuzznuc. Use the original source fasta
> >
> >  > sequence name as the common key for the merge. If both data are in BED
> >
> >  > format, that would be ideal and make the following steps possible. You
> >
> >  > may need to split the file based on whether the original fasta sequence
> >
> >  > came from the positive or negative strand to run "b" and "c" below
> >
> >  > separately.
> >
> >  > b) Use "Text Manipulation -> Compute an expression on every row" to
> >
> >  > create new coordinates. For example, if your data is on the positive
> >
> >  > strand, and base 1 in your fasta file was genomic coordinate 100, and
> >
> >  > the alignment from fuzznuc started at base 5 (local coordinate == "4" if
> >
> >  > in BED format with a zero-based start), then the new genomic start
> >
> >  > coordinate would be [100 + 4)] = 104. Do this for both start and stop.
> >
> >  > c) Adjust the logic for "b" if any of your original fasta sequences are
> >
> >  > from the negative strand, on the negative strand portion of your data
> >
> >  > ("b" would be run on just the positive strand portion of your data).
> >
> >  > d) arrange/cut the resulting file down into a standard BED format to
> >
> >  > remove the local coordinates and keep the genomic coordinates, using the
> >
> >  > original chromosome names.
> >
> >  > e) once the logic for the calculations is worked out, save the process
> >
> >  > into a workflow for use again.
> >
> >  >
> >
> >  > Hopefully this helps,
> >
> >  >
> >
> >  > Best,
> >
> >  >
> >
> >  > Jen
> >
> >  > Galaxy team
> >
> >  >
> >
> >  > On 5/13/11 9:32 AM, Robert Curtis Hendrickson wrote:
> >
> >  >> Folks,
> >
> >  >>
> >
> >  >> I wanted to scan the 2kb upstream of a list of human gene isoforms
> > for TFBS using fuzznuc. I was able to
> >
> >  >> "Get Data"> "UCSC Main"> "As sequence" and get my sequences
> >
> >  >> "EMBOSS"> fuzznuc ran fine, and output the hits
> >
> >  >>
> >
> >  >> HOWEVER, fuzznuc lost the genomic position information that UCSC has
> > put after a space in the sequence headers of the FASTA file. It only
> > provided offsets within the fasta.
> >
> >  >>
> >
> >  >> http://main.g2.bx.psu.edu/u/curtish-uab/h/ucsc-fuzznuc-ucsc-broken
> >
> >  >>
> >
> >  >> Thus, when I converted the fuzznuc output back to a BED file and
> > tried to visualize the hits in UCSC browser, it failed with "invalid BED
> > File".
> >
> >  >> I tried fuzznuc with output: seqtable, feattable and gff3, but in
> > all cases the genomic position was missing, and being a bit of Galaxy
> > novice, I couldn't figure out how to get the output back to UCSC to
> > visualize the hits.
> >
> >  >>
> >
> >  >> Can anyone tell me how to link up these tools correctly, or share a
> > history with some other tool set that accomplishes this goal?
> >
> >  >>
> >
> >  >> Regards,
> >
> >  >> Curtis
> >
> >  >>
> >
> >  >> Research Associate
> >
> >  >> Center for Clinical and Translational Science
> >
> >  >> University of Alabama at Birmingham
> >
> >  >>
> >
> >  >> ___________________________________________________________
> >
> >  >> The Galaxy User list should be used for the discussion of
> >
> >  >> Galaxy analysis and other features on the public server
> >
> >  >> at usegalaxy.org. Please keep all replies on the list by
> >
> >  >> using "reply all" in your mail client. For discussion of
> >
> >  >> local Galaxy instances and the Galaxy source code, please
> >
> >  >> use the Galaxy Development list:
> >
> >  >>
> >
> >  >> http://lists.bx.psu.edu/listinfo/galaxy-dev
> >
> >  >>
> >
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> >
> >  >> please use the interface at:
> >
> >  >>
> >
> >  >> http://lists.bx.psu.edu/
> >
> >  >
> >
> > --
> >
> > Jennifer Jackson
> >
> > http://usegalaxy.org
> >
> > http://galaxyproject.org
> >
> 
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org

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