User: apozhitkov

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apozhitkov50
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50
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3 months, 4 weeks ago
Joined:
9 months, 2 weeks 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 5 months ago by apozhitkov50
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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 5 months ago by apozhitkov50 • updated 5 months ago by Jennifer Hillman Jackson23k
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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 9 months ago by apozhitkov50
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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 9 months ago by apozhitkov50
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Forum: An entertaining read about BWA, Picard, GATK
... **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 ...
galaxy software error forum bwa bam samtools written 9 months ago by apozhitkov50 • updated 5 months ago by linying91140

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