Question: Blast
0
gravatar for Madison-Villar, Mercedita J
8.1 years ago by
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
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ADD COMMENTlink written 8.1 years ago by Madison-Villar, Mercedita J20
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