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
>
> ___________________________________________________________
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-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org

___________________________________________________________
The Galaxy User list should be used for the discussion of
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