Dear all,
given 3 samples, 1 control and 2 treated replicates when I do
cuffcompare to produce the gtf input for cuffdiff, do I have to run it
with or without the cufflink control?
E.g. Cuffcompare with only my 2 treated replicates?--use
this gtf to run cuffdiff
Cuffcompare 1
Dear all,
I managed to upload to Galaxy a genome of interest in .fasta format
from NCIB website.
However, Galaxy does not recognize it as input to run Tophat...
Wht format has to be to be used as referece genome for tophat?and how
can i convert it?
Any suggestion?
thanks,
ib
Hello,
Could someone provide instructions for installing galaxy on a Mac OS 10.7? The
instructions provided by galaxy start off by asking me to check my python
version, but I don't know how to do that. I figure someone has step-by-step
instructions or a screen cast?
Thank you,
Edward
I have problem to split a paired-end FASTQ dataset into two separate datasets.
In order to explain the problem clearly, I list the detail of what I did with
my dataset:
Step 1) My aim is to compare datasets for the differential alternative
splicing. I downloaded paired-end datasets at FASTQ
Both responses worked for checking python version, but trying to download gave
an error:
Install Galaxy on Mac OS10.7
1. Open Applications/Utilities/Terminal.app
2. Check Python version by pasting in python -V, no quotes, and hit return
response = Python 2.7.1
3. Get Galaxy by pasting in
Hi Jen,
Yes, it is best to assume I know nothing about programming. I installed
Mercurial, but don't know how to check that it was successful other than it
said so. Removing % helped, but said I do not have permission:
Install Galaxy on Mac OS10.7
1. Open Applications/Utilities/Terminal.app
2.
I was wondering if anyone could comment on how memory/computational intensive a
local instal of Galaxy is? What type of computer (especially Macs) is needed
for a local install to run fairly well?
Thanks for any info--- Diana
**
Diana Cox-Foster, Professor
Hello Yan,
This workflow can be used to sort SAM input for Cufflinks:
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2
Best,
Jen
Galaxy team
On 8/10/12 3:13 AM, Yan He wrote:
Hi everyone,
After mapping my RNA-seq data to the reference transcriptome using Bowtie, I
Hello Irene,
This wiki has the formatting details, including a screencast for genome
prep, and many tips for correcting format problems that use Galaxy's
tools whenever possible:
http://wiki.g2.bx.psu.edu/Learn/CustomGenomes#Screencasts_.26_Tutorials
watch Custom Genome Prep
Hi Edward,
Sorry, the https is probably also a problem. I thought about
commenting about that before, but was wasn't sure about how much help
you would need exactly or if you were logged into bitbucket or not. So
please use this:
prompt$ hg clone http://bitbucket.org/galaxy/galaxy-dist
Thanks Jen, Hans, and Scott,
I have it running on my laptop now and here are the steps I followed:
Install Galaxy on MacBook Pro OS10.7.4 (08-10-2012)
• Install Mercurial http://mercurial.selenic.com/wiki/
• Open Applications/Utilities/Terminal.app
• Confirm Mercurial
I am new to the NGS analysis. I need help to solve this problem.
As shown in my previous emial/question shown below, I have some paired-end
datasets at FASTQ format, and I have problem to split each of these datasets
into two datasets (one forward and one reverse).
Jennifer instructed me
I am new to the NGS analysis. I need help to solve this problem.
As shown in my previous emial/question shown below, I have some paired-end
datasets at FASTQ format, and I have problem to split each of these datasets
into two datasets (one forward and one reverse).
Jennifer instructed me
Hello Ted,
Workflows are included in the Galaxy Main Tool Shed
http://toolshed.g2.bx.psu.edu/
-- Search for workflows
Documentation is in this wiki (see #22, 23, 24):
http://wiki.g2.bx.psu.edu/Tool%20Shed
Other current information about workflow development can be found in the
Dear Sir / Madam,
I'm new to Galaxy. Is there any way to extract all CpG-SNPs from
dbSNP135 using Galaxy (preferably as a BED file, but a text file will
do)? I tried to figure out myself, but came up short... All help is
much appreciated!
Sincerely, RH
Hi Edward
I am moving your e-mail to 'galaxy-dev' since it's about a local Galaxy
instance.
I don't think there are any differences between installing Galaxy on
Linux and Mac OS X. Hence you can follow the step-by-step instructions
on the wiki (well, there are actually only two steps anyway...):
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