Question: Blast
0
Madison-Villar, Mercedita J • 20 wrote:
Hi...
I have an analysis of 18,000,000 + sequences (X4) blasting through the
HTGS database. Is there anyway to blast to a subset of this database
to make the analysis much more speedy? Is the also a way to know if
the analysis is working...ie periodic updates? I have had issues
before with uploading large files where there is an error, but no
error message. The data will look like its uploading when in fact it
isnt. I just dont want to have to wait a week or weeks and find out
the analysis is never going to end.
Thanks!!
Mersee
Mersee Madison-Villar
PhD Student, UT Arlington
Lab/Office B01
Genomics, Speciation, and Evolutionary Biology
"If evolution is outlawed, only outlaws will evolve"- Jello Biafra
________________________________________
To: Andigoni Malousi
Cc: galaxy-user@bx.psu.edu
Subject: Re: [galaxy-user] problem report!!
Hi Andigoni,
I'm unable to reproduce the issue reported by you. I used the BED file
sent by you as attachment and fetched sequences on it. The sequences
produced were of the same lengths as in the BED file.
Also, I computed summary statistics for the lengths of your BED
intervals - the mean and median lengths were 19790 bp and 3466 bp
respectively. Since you mention that you expect the constitutive exons
to be 100-200 bp long, I'm guessing there might be a problem in one of
the steps prior to the subtraction step in your pipeline.
If you can share your history with me
(guru@psu.edu<mailto:guru@psu.edu>), I can take a look at what might
be going on. Here's how to do it:
-go to the Options menu above your current history, select "Saved
Histories"
-go to the pull-down menu for the problematic history and select
"Share or Publish"
-share the history with me by clicking on "share with a user" and
entering my email address: guru@psu.edu<mailto:guru@psu.edu>.
Thanks for using Galaxy,
Guru
Galaxy team.
Dear Galaxy member,
I'm sending you this e-mail because of a problem I have in fetching
sequences. I used Galaxy to fetch sequences corresponding to
alternatively spliced exons as well as constitutive exons.
Here they are the steps I followed to do that:
First, I extracted the coordinates of the ref genes from whole human
genome:
1. I selected Get Data -> UCSC table browser
2. Genome: "Human", assembly: "Feb. 2009", Group: "Genes and Gene
Prediction Tracks", Track:"RefSeq genes".
3. Filter: (+) region: Genome
4. "get output" and "Exons plus 0 bases
"
Second, I extracted the coordinates of alternative splicing events
1. I selected "Get Data" -> "UCSC Main table browser".
2. Genome: "Human", assembly: "Feb. 2009", Group: "Genes and Gene
Prediction Tracks", Track:"Alt Events".
3. Filter: (+) region: Genome
Then, I stored the outcome of these two processes in BED format. To
extract the coordinates of the constitutive exons I used the Subtract
operation in "Operate on Genomic Intervals"
1. Substract: Alternative splicing events From: Ref genes
2. "Intervals with no overlap"
3. Stored the constitutive exon coordinates in BED format