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
Hi galaxy users,
Am I right in thinking there is no tool for sorting a sam/bam file in Galaxy?
I think this has probably been discussed before, sorry. I just want to
check I haven't missed anything, since sibling tools from e.g. the
samtools and picard suites are wrapped.
P: 03 903 53357
M: 0414 854 759
I'm experimenting with Galaxy Cloudman, and could use a simple workflow to
a) test that Galaxy is working ok
b) put some significant load on a Galaxy server so that it shows in the
load diagram, ie. as below
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?
Does anyone know how to get alignment stats from Bowtie on Galaxy? I
would like to know what percentage of total reads from my dataset is
I know if you run Bowtie using the command line, it gives you the
report. However, I could not find percent alignment on Galaxy.
Thanks in advance for the help!