User: David Joly

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David Joly100
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5 years, 5 months ago
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7 years, 1 month ago
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Posts by David Joly

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Comment: C: Teaching Using Galaxy
... I was pretty much interested in Bio-Linux. However, the version of Galaxy that comes with it is already outdated and there is no easy way to update it. It is possible to delete it and re-install a newer version, this would be another possibility... Le 2013-04-25 ŕ 05:50, Hans-Rudolf Hotz a écrit : ...
written 5.5 years ago by David Joly100
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Comment: C: Teaching Using Galaxy
... Thanks Dave! The focus is clearly more like your second description. The course is not intended to show them how to use command lines, or how to navigate in a UNIX environment and how to program. In fact, I think some would call what I have in mind more of a "computational biology" course than a "b ...
written 5.5 years ago by David Joly100
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Teaching Using Galaxy
... Hi everybody! I am currently creating a "bioinformatics" course for undergraduate (biology students with no knowledge of programming). I would like to use Galaxy as their everyday platform where they would learn the basics and use the appropriate tools (BLAST and databases, multiple alignment, phyl ...
galaxy written 5.5 years ago by David Joly100 • updated 5.5 years ago by Dave Clements ♦♦ 2.4k
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Fwd: Installing New Tools From The Tool Shed
... Thanks Dannon! One step closer (I thought closing the browser would be enough to restart galaxy, but obviously, I had to reboot the computer)... But now it says: ValueError: too many values to unpack 2013/2/13 Dannon Baker ...
galaxy written 5.7 years ago by David Joly100
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Installing New Tools From The Tool Shed
... Hi! Ok, I know many people had the same issue, but I just can't figure what's going on. I'm quite new about using a local instance of Galaxy and I'm trying to figure how to install a tool from the tool shed. Reading the tutorial (Installing Galaxy tool shed repository tools into a local Galaxy ins ...
galaxy written 5.7 years ago by David Joly100
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Trinity
... I want to run Trinity on the "test" instance of Galaxy, but there seems to be a problem. The analysis complete very quickly and I've got no assembled transcripts. In the log file created by Trinity, there is one line: /var/spool/torque/mom_priv/jobs/1204985.thumper.g2.bx.psu.edu.SC: 11: Trinity.pl ...
galaxy written 7.1 years ago by David Joly100 • updated 7.1 years ago by Jennifer Hillman Jackson25k
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Comment: C: Aachanges
... Thanks! I decided to install a local instance of Galaxy. The installation went fine, but now I'm not sure how to add a custom genome. I found some information in past comments on the user list but I'm not sure I understand everything. All I've got is a fasta file with all my supercontigs and a gtf f ...
written 7.1 years ago by David Joly100
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Aachanges
... Hi everybody, Maybe a dumb question but does someone know if we can use the aaChanges tool on a custom genome? I have my SNP dataset and my gene dataset but I can only assign them to one of the genome build already in UCSC... I am using the web server of galaxy. Do I need to install my own local in ...
galaxy written 7.2 years ago by David Joly100 • updated 7.2 years ago by Jennifer Hillman Jackson25k
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Cufflinks Quartile Normalization
... Can someone help me understanding the quartile normalization in Cufflinks? I read different threads in which they reported that the FPKM values were inflated after normalization (-N) but most people didn't report their values so I don't know how big the inflation should be... In my case, the differ ...
cufflinks rna-seq written 7.2 years ago by David Joly100 • updated 7.1 years ago by Jeremy Goecks2.2k
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Unspecified Genome Build
... I'm trying to use the "Extract Genomic DNA" feature from "Fetch Sequences" on Cufflinks-assembled transcripts, using a custom genome. However, when I specify "History" as the "Source for Genomic Data" and a fasta file as the reference file, I still get the "Unspecified genome build" error. I read so ...
cufflinks rna-seq written 7.2 years ago by David Joly100 • updated 7.2 years ago by Jennifer Hillman Jackson25k

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