User: Philipe Moncuquet

Reputation:
40
Status:
New User
Location:
Australia
Last seen:
3 years ago
Joined:
5 years, 7 months ago
Email:
p************@gmail.com

Posts by Philipe Moncuquet

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Combining Reads from 2 Lanes
... Hi,   If you have no interest in the technical replication itself I would suggest to merge files at the very beginning of your analysis. You could do so with something as simple as 'Concatenate datasets' in the 'Text manipulation' section I guess. Happy to be corrected.   Philip ...
written 3.1 years ago by Philipe Moncuquet40
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Visualization issue in Trackster on local instance
... Hi, I have added my comment to the following post (https://biostar.usegalaxy.org/p/7294/) but was unsure of the visibility.  I am trying to visualize some NGS read alignment file in trackster on my local instance. I have tested the same visualization on the main instance and it worked well so ther ...
reference trackster visualization written 3.1 years ago by Philipe Moncuquet40
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Answer: A: Visualizing BowTie2 BAM File?
... Hi there, I am having the same problem here. I work on the hg19 build with some reads fro chr20 and no matter how deep I zoom in I can't see nucleotides sequence as per the example shown by Bjoern. I have check that the build is well recognised, when I had a vcf file track with variant I am actuall ...
written 3.1 years ago by Philipe Moncuquet40
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Comment: C: Gatk2 Galaxy Wrapper Available, Testing And Help Needed
... I just realized that for reference genome to be added in gatk2, an entry at to be created for that specific .loc files in the tool_data_table_conf.xml file. ...
written 3.1 years ago by Philipe Moncuquet40
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Answer: A: Need help with "Mark Duplicate reads" tool
... We cannot help you if you don't explain the problem. Do you have a problem with the installation from the toolshed, the tool usage or some results you don't understand ? Please provide more details. ...
written 3.5 years ago by Philipe Moncuquet40
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Answer: A: Denovo with tophat
... You might want to read this http://bioinformatics.oxfordjournals.org/content/25/9/1105.long ...
written 3.5 years ago by Philipe Moncuquet40
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Data collection and Tophat2
... Hi, I am trying to play with data collection (developped by John Chilton) and I am confused on how to do the Tophat2 step. I have 5 conditions (triplicates) paired end data. So I have 30 files that I use to create a 'list of dataset pairs'. I end up with that new entity containing 15 pairs. It wor ...
collection tophat2 rna-seq written 3.5 years ago by Philipe Moncuquet40 • updated 3.5 years ago by Bjoern Gruening5.0k
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Comment: C: Need help with "Compare two Datasets" tool
... Are you working on 'main' ? What is the error ? What are the inputs ? ...
written 3.5 years ago by Philipe Moncuquet40
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Migration of universe_wsgi.ini to galaxy.ini
... Hi, I am trying to clean up our Galaxy instance. I have noticed to recent effort to put configuration files in a sub-directory.  I am wondering what is the best way to migrate from the old configuration file (universe_wsgi.ini) to the new one (galaxy.ini) and how will Galaxy handles the presence o ...
administration written 3.5 years ago by Philipe Moncuquet40 • updated 3.5 years ago by Bjoern Gruening5.0k
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Answer: A: Gatk Not Running
... Hi, I have encountered the same kind of errors. When I update the loc files link to GATK, some of the tools display the reference genomes I added and some not. It seems that the galaxy wrapper for GATK 1.6 is not very functional. GATK don't really care because they are not supporting it any more, e ...
written 5.5 years ago by Philipe Moncuquet40

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