User: Loraine, Ann

gravatar for Loraine, Ann
Loraine, Ann150
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3 years, 5 months ago
Joined:
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Posts by Loraine, Ann

<prev • 16 results • page 1 of 2 • next >
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News: Learn how to use IGB with Galaxy for RNA-Seq - Nov 12, 2014
... Hi all! Please join us on: Wed Nov 12, 2014 11:30-12:00 pm EST for LIVE tutorial on using Galaxy and Integrated Genome Browser for RNA-Seq. For info, see: Live on-line tutorial using Integrated Genome Browser (November 12, 2014 11:30am-12pm EST) Please spread the word! Best, Ann ...
news galaxy igb rna-seq written 3.8 years ago by Loraine, Ann150 • updated 3.8 years ago by Jennifer Hillman Jackson25k
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Answer: A: Table browser output going to test.galaxyproject.org
... Sorry! I spoke too soon. All I needed to do was reset my preferences at UCSC. ...
written 4.2 years ago by Loraine, Ann150
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Table browser output going to test.galaxyproject.org
... Hi, I'm using the Table Browser at UCSC to make files and send the output to Galaxy using the "Send to output to" checkbox available on the query page. (I checked the Galaxy option.) The output of the query is getting sent to test.galaxyproject.org instead of the main Galaxy at usegalaxy.org. Can ...
galaxy ucsc written 4.2 years ago by Loraine, Ann150
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poster dimensions for Galaxy Community Conference, Baltimore
... Please post a link to the info if you have it! What are the poster dimensions for upcoming June 2014 Galaxy Community Conference? Thanks! Ann   ...
conference written 4.2 years ago by Loraine, Ann150 • updated 4.2 years ago by Dave Clements ♦♦ 2.4k
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Comment: C: Get Wig File After Tophat
... Thank you for the reminder and the encouraging words! We just released IGB 6.5 (many improvements!) and are planning what to do next. Top on the list is to do a better job of supporting Galaxy users by making it possible to view your "BAM" files in IGB without having to download them first. I wil ...
written 7.3 years ago by Loraine, Ann150
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Answer: A: Bam Files
... Are you downloading the łBAI˛ index file, as well? That might be the problem. Best, Ann -- Ann Loraine Associate Professor Dept. of Bioinformatics and Genomics, UNCC North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 www.transvar.org ...
written 7.3 years ago by Loraine, Ann150
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Answer: A: Mapping Illumina Reads Using Lastz
... Hi, If you download the BAM file and it's index ("BAI") file onto your desktop, you should be able to open it directly in Integrated Genome Browser. Just be sure to put the BAM and its BAI file in the same folder. If you run into any problems, please let us know. You can post a message on the IGB ...
written 7.4 years ago by Loraine, Ann150
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Comment: C: Replicates
... Hello, I like your approach of running the alignment tools with liberal settings and then filtering the results into different categories. This discussion reminds me of how in expression microarray analysis, we face uncertainty as to what molecules (exactly) are hybridizing to the probes on a chi ...
written 7.5 years ago by Loraine, Ann150
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Comment: C: Replicates
... Hello, I like your approach of running the alignment tools with liberal settings and then filtering the results into different categories. This discussion reminds me of how in expression microarray analysis, we face uncertainty as to what molecules (exactly) are hybridizing to the probes on a chip ...
written 7.5 years ago by Loraine, Ann150
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Comment: C: Get Wig File After Tophat
... I'm a fan of viewing "coverage.wig" files - they give a nice summary of read distribution over a chromosome. What I like about the "coverage.wig" file is that it captures the full read depth at every base. TDF does something different - it summarizes over (relatively) large regions. (But this can b ...
written 7.5 years ago by Loraine, Ann150

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