I am a new user of galaxy. i met a problem and didnot find similar
question in FAQ. I wanted to upload the data from DDBJ DRA dataset to
galaxy through UTL method. The file is around 800M. However after
uploading, the FASTQ file was just around 2M. So I wanted know whether
it is possible to upload a large file to galaxy through URL method? or
I should download the file to my pc and then uploading to galaxy
through FTP method.
Would you please perform the following new genome load?
All the necessary resource files can be found and downloaded at:
Professor of Plant Molecular Biology
Penn State University
Department of Horticulture
422 Life Sciences Building
University Park, PA 16802-5807
Phone 814 863-7957
Web Site: http://guiltinanlab.cas.psu.edu
I uploaded a tab-delimited file(this was constructed within R using
write.table) into Galaxy with chr, start, end, and esembl_TSS_name. Whilst
I am able to use fetch sequence function, currently not able to include the
Esembl ID in the FASTA output. I am able to include the Ensembl name in
the interval format but not in FASTA format.
I am trying to join two groomed fastq files from a paired-end Illumina
read using the fastq joiner tool. The drop-down menus correctly
identify the groomed fastq files, but after cranking for a few minutes
the tool produces empty output:
"FASTQ joiner on data 5 and data 4
format: fastqsanger, database: ?
Info: There were 3497909 known sequence reads not utilized.
Joined 0 of 3497909 read pairs (0.00%)."
The files have the same number of reads (3497909), reads have the same
number of bases (102), and the joiner tool doesn't have any options
(other than choosing the two files to join). Can anyone tell me what
I'm doing wrong?
Matthew D. Herron, PhD
Department of Zoology
University of British Columbia
I using operate on genomic intervals on some data and it always seems to ignore the strand information. Am I missing something or does "operate of genomic intervals" disregard strand information? Is there a tool that does the inner join function and takes into account strand information?
Stephen Eacker, Ph.D.
Institute for Cell Engineering
Johns Hopkins Medical Institute
I want to use cufflinks handle the results of Tophat. Cufflinks uses FPKM to normalize the expression data. I think FPKM is for pair-end reads. right? My reads are single-end. Is it right if I use FPKM?
Thank you very much!
I have not been using Galaxy for a few months an it seems that a least
one of my history was deleted.
I assume it is because of inactivity for too long/exceeding the new quotas.
Would there be by chance a a way to re-access it temporarily to be able
to download some of that data or has it been totally erased?
we are running a local Galaxy server, administered by a bioinformatics
core group. Our end users increasingly come to us with sets of large
NGS files that they can't upload to Galaxy on their own through a web
browser. We copy their data to a Galaxy filesystem and upload into data
libraries from there using the admin interface. However, the users
would prefer to be able get their data onto the server on their own.
What's the best solution to that? Should we set up FTP upload? Are
there other tricks? Any advice would be appreciated.
Yury V. Bukhman, Ph.D.
Associate Scientist, Bioinformatics Group Leader
Great Lakes Bioenergy Research Center
University of Wisconsin - Madison
445 Henry Mall, Rm. 513
Madison, WI 53706, USA
Phone: 608-890-2680 Fax: 608-890-2427
To Whom It May Concern,
I am curious if there is a tool within Galaxy to generate a set of random intervals from a particular genome similar to the "Random Intervals" tool within the ENCODE tools? I am using the "Aggregate datapoints" tool to get phastCons conservation scores for peaks from ChIP-Seq data. I would like to compare these scores to a random expectation so would like to be able to use a Random Intervals-like tool to generate a set of random positions to compare to the experimental set.
Vincent J. Lynch, Associate Research Scientist
Department of Ecology and Evolutionary Biology & Yale Systems Biology Institute
"There is a grandeur in this view of life, with its several powers,
having been originally breathed into a few forms or into one; and that
whilst this planet has gone on cycling according to the fixed laws of
gravity, from so simple a beginning endless forms most beautiful and most
wonderful have been, and are being, evolved." -C. Darwin, 1859
I have illumina ChipSeq data in txt format with this structure:
Can I convert into Fastq format?If so, how can I?
Furthermore, after using Map with Bowtie for Illumina, how can I use
Analysis of ChIP-Seq) if I have two files for IP samples and two files for
Thank you so much.