NGS with Arabidopsis thaliana built-in-index
by Tom Smith
Hi all,
I've been having trouble running my Arabidopsis thaliana NGS pipeline in galaxy. Specifically, tophat alignment to the built-in-index worked fine (visual assessment in IGV) but I couldn't get cufflinks/Cuffduiff to run using the same annotation.gtf file I'd used in the alignment. Error message = Error running cufflinks. return code = -11 cufflinks: /lib64/libz.so.1.
Cufflinks/cuffdiff would run without the annotation file and give a differential expression output but without the annotation file the gene_id was meaningless (XLOC_000001 etc) and all I had was a locus for a region with differential expression.
After a lot of frustration I re ran the alignment using a custom built genome and annotation file from Illumina: http://cufflinks.cbcb.umd.edu/igenomes.html and hey presto, cufflinks/cuffdiff work fine. I did try altering using both chr1 and 1 for chromosome name as a discord between the chromosome naming seemed to frequently be a problem. Apart from this, what other reasons could there be for the built-in-index not working with annotation.gtf files? Is this an issue with the built-in-index (Mouse-ear Cress (Arabidopsis thaliana): Arabidopsis_thaliana_TAIR10)?
Cheers,
Tom SmithUniversity of York, UK
8 years, 12 months
how to download onto a server?
by Loraine, Ann
Hi,
I would like to transfer results files (e.g., accepted_hits.bam) from my Galaxy history onto a server — not my local computer.
How do I do that?
Best,
Ann
-------------------------------
Ann Loraine, Ph.D.
Associate Professor
Department of Bioinformatics and Genomics
University of North Carolina at Charlotte
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
704-250-5750
aloraine(a)uncc.edu
http://www.transvar.org
http://www.bioviz.org
http://www.uncc.edu
8 years, 12 months
Boxplot error.
by 柴田 弘紀
Hello,
I'm pretty new for Galaxy.
I am running a local Galaxy server on Mac. I tried to draw a boxplot from summary statistics created from groomed fastq data.
Then I got error message as follows:
An error occurred running this job: gnuplot> set term png size 2048,768 ^ line 0: unknown or ambiguous terminal type; type just 'set terminal' for a list
line 0: warning: Too many axis ticks requested (>1e+02) Error running gnuplot.
I believe gnuplot was appropriately installed using MacPorts (confrimed it starts when I type "gnuplot" on terminal). I also installed libpng by Macports and now "png" is listed when I type "set terminal" in gnuplot for a list.
How can I help it???
Thank you very much.
Hiroki
9 years
History Pane empty?
by jason gagliano
Hi
I just had a quick question. My History pane to the right of my Galaxy
account on the web suddenly was empty when I logged in. I noticed that I
can still find all my datasets under "Saved History" or "Saved Datasets"
but nothing will show up now in the history pane. This is true even when I
upload a new data set.
Any thoughts on the problem and a solution?
Thanks
Jason
P.S. I have read all I could find on the topic in the help sections before
asking this question. But I could not find anything that worked for me
(like simply deleting cookies). I am relating this to say that I am trying
to be a good citizen by reading first and then asking questions :0)
9 years
