February 2012 - galaxy-user - lists.galaxyproject.org

bx.seq.twobit - write a 2bit file?
by Amit Indap 02 Feb '12

02 Feb '12

Hi, I had a question about the bx python API. I'm using its twobit API to read sequence intervals from a two bit file. If I had sequence I wanted to write to a 2bit file, is there a way to do that with bx-python API? Otherwise, I was going to use FaToTwoBit program from jksrc, but it would be nice if there is a way I can do it from python. Thanks for the help! Amit

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The size of the history
by 杨继文 01 Feb '12

01 Feb '12

Hi all, First I would like to thank you for your fast replies to my questions. As you know, at top right corner of Galaxy window, there are records of the history size and how many percentage of memory space has been used. I found that the number in the records only increases, but doesn't decrease after I delete files permanently. DId I miss something? How to let the record show the real size of the histories? Thanks in advance. Greetings, Jiwen

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FTP and Biomart
by 杨继文 01 Feb '12

01 Feb '12

Hi All, Today I have problem to use FTP to upload data to Galaxy. I used Filezilla software and the server name "main.g2.bx.psu.edu", but I can not connect to the server. Something wrong with my operation? Also, when I tried to get data from Biomart to Galaxy, I got the error warning "the uploaded file contains unappropriate HTML links " Hope you can tell me if I did something wrong. Thanks Jiwen

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A simple operation didn't work out
by 杨继文 01 Feb '12

01 Feb '12

Hi All, I got a bit disappointed when I failed in the following operation which seems to be simple. I uploaded mouse annotation/reference gene sets (GTF format) to Galaxy. The file is located at ftp://ftp.ensembl.org/pub/release-65/gtf/mus_musculus/. As far as I know, GTF file is tab delimited, thus I used "Filter and Sort" --"filter" With following condition:C1 == 19 . column 1 is where chromosomes are located. I want to pick up all lines which belong to chromosome19. However, I only got an empty file. I know this is not a bit issue to discuss here. But I still hope you can help me figure out what 's wrong. Thanks Jiwen

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clustering algorithm in Galaxy
by Daniel Elleder 01 Feb '12

01 Feb '12

Is there a good read clustering algorithm available in Galaxy? Specifically for 454 and Ion Torrent reads. In the Galaxy e-mail archive I see mentions of dnaclust, but I cannot find it in the menus.

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