User: apozhitkov

gravatar for apozhitkov
apozhitkov60
Reputation:
60
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New User
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Last seen:
12 months ago
Joined:
1 year, 5 months ago
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a*********@coh.org

Posts by apozhitkov

<prev • 5 results • page 1 of 1 • next >
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Comment: A: cufflinks on Rna -seq data not working
... Describe your steps in more detail. I had other problems with cufflinks like producing FPKMs all zero, but at least it ran. ...
written 14 months ago by apozhitkov60
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GALAXY_SLOTS and slashes
... Here is my experience with an exercise to make Galaxy utilize a multi-core / multi-processor environment of our server. Our setup is an Azure 16-cpu machine, which contains the latest release of Galaxy (17.05). My goal was to enable multithreading for the mapping tools such as RNA-STAR and TopHat ...
tophat multi-processor multi-core rna-seq written 14 months ago by apozhitkov60 • updated 14 months ago by Jennifer Hillman Jackson25k
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Comment: C: An entertaining read about BWA, Picard, GATK
... Hi Guy, Thanks for the hints! I haven't heard of the dockers before... As for the GATK, indeed, the Broad institute makes you sign something that you are at a non-profit or at a university. It applies to me, so I got their stuff... Alex. ...
written 17 months ago by apozhitkov60
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Comment: C: An entertaining read about BWA, Picard, GATK
... Hi Martin, The most difficult part was digging through the maze of the xml files that determine the tool parameters, configuration and requirements. I have two suggestions. First, the process of finding and adjusting tool configuration needs to be much more compact and uniform. Say ONE xml file of ...
written 17 months ago by apozhitkov60
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GATK (deprecated tools)
... **Objective** The objective is to implement a variant discovery and annotation pipeline similar to one published by Valle et al., (BMC Bioinformatics 2016, 17, 341) and compare the results with those produced by NextGene. The NextGene results were experimentally verified with known variants as wel ...
gatk galaxy written 17 months ago by apozhitkov60 • updated 3 months ago by gintotomticket0

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