User: leontp587

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leontp58750
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United States
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4 years ago
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4 years ago
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Posts by leontp587

<prev • 5 results • page 1 of 1 • next >
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Comment: A: bowtie2 out of memory
... Thanks Jen! I took it up to 13GB of memory and it worked very well. ...
written 4.0 years ago by leontp58750
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bowtie2 out of memory
... I'm trying to run bowtie2 in galaxy on my own centos installation to align paired end data to the hg19 reference. I get an out of memory error: bowtie2 -p ${GALAXY_SLOTS:-4} -x /home/leon/ref_data/bowtie2/hg19/hg19 -1 /home/leon/genome_data/sra/ERR010982/ERR010982_1.fastq -2 /home/leon/genome_data/ ...
bowtie2 galaxy scaling local memory written 4.0 years ago by leontp58750
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Answer: A: Cannot add hg19 reference genome to bowtie2 on galaxy
... Finally got it to work! Apparently the solution is to modify the tool_data_table_conf.xml file and add the lines: <table name="bowtie2_indexes" comment_char="#">             <columns>value, dbkey, name, path</columns>             <file path="tool-data/bowtie2_indices.loc" /> ...
written 4.0 years ago by leontp58750
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Answer: A: Cannot add hg19 reference genome to bowtie2 on galaxy
... Hi Jennifer, Thanks for your reply, but I'm even more confused. 1) For the builds.txt file, I checked /home/leon/galaxy-dist/tool-data/shared/ucsc/builds.txt, which already has a line for hg19: hg19    Human Feb. 2009 (GRCh37/hg19) (hg19) Given that it already has a line hg19 from the default ins ...
written 4.0 years ago by leontp58750
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Cannot add hg19 reference genome to bowtie2 on galaxy
... I tried to bring up a quick instance of galaxy up on my own linux server to align some fastq reads to the hg19 genome. For some reason, I cannot get the hg19 reference genome to show up in the bowtie2 reference genome dropdown in galaxy. Below are the steps I took, but after restarting the server th ...
genomes indexes galaxy local bowtie2 written 4.0 years ago by leontp58750 • updated 4.0 years ago by Jennifer Hillman Jackson25k

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Scholar 4.0 years ago, created an answer that has been accepted. For A: Cannot add hg19 reference genome to bowtie2 on galaxy

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