Hi,
I have been trying to upload my RNA-seq data files (~20 Gb total) via FTP
using my account in Galaxy. But I could not connect to the server. The
following message showed up:
*Error: Critical error*
*Error: Could not connect to server*
Could you suggest any idea to overcome this problem?
Thank
Hi all,
I just finished uploading 2 files via FTP and I have some more files to be
uploaded. After an Internet disconnection, I got the same problem like
Delong had. I got this message:
530 Sorry, the maximum number of clients (3) for this user are already
connected
Error: Critical error
Error:
Hi guys,
I am trying to examine gene differential expression in my mouse samples
using :
Cufflink CuffmergeCuffdiff
The output from Cuffdiff shows only gene id, but not gene name:
test_id gene_idgenelocussample_1
sample_2
XLOC_01XLOC_01-
Hi all,
I have been working on RNA-seq data analysis using TopHat and Cuffdiff. One
of the problem I have is to define the cutoff RPKM value to tell whether a
gene is expressed from the background noise?.
Could anybody give me a suggestion?
Thank you
Thanh
Hi,
I ran TopHat on Galaxy for my RNA-seq data. I want to analyze TopHat's
output files, such as percentage of reads mapped to the genome...but I am
not sure how to do that.
I am also trying to visualize the BAM file by IGB but the following error
message appears : Failed to authenticate to the
, let us know about the second,
Take care,
Jen
Galaxy team
On 7/14/13 1:47 PM, Hoang, Thanh wrote:
Hi,
I ran TopHat on Galaxy for my RNA-seq data. I want to analyze TopHat's
output files, such as percentage of reads mapped to the genome...but I am
not sure how to do that.
I am also
Hi all,
I am working on RNA-seq using TopHat/Cufflink/Cuffdiff for differential
gene expression and new gene discovery ( this is what I am interested in).
However, I found many genes that are repeated in the Cuffdiff's ouput.
These are the same genes and at the exact the same locus. There should
Hi all,
I would like to analyze my miRNA sequencing analysis from mouse tissue. I
have not any idea which tools or pipeline work best. Do you have any
suggestion?
Regards
Thanh
___
The Galaxy User list should be used for the discussion of
documentation, that you
can review to see if the tool is a good fit for what you want to do (if it
is not expression analysis anymore, or you want to try something different
like DESeq).
http://toolshed.g2.bx.psu.edu/repository
Hopefully this helps,
Jen
Galaxy team
On 9/18/13 10:19 AM, Hoang, Thanh
Hi all,
I am analyzing miRNA sequencing now. My data is 51bp, single -ended and ~5
M reads. I want to remove the adapter sequences from the reads before
mapping to the genomes/known miRNA database.
My 3' adapter sequence is : 5-AGATCGGAAGAGCACACGTCT-3. I found that many
reads only contain part of
Hi all,
I want to to map my sequencing reads to miRNA reference database . Anyone
know how to convert RNA to DNA in FASTA format ( U to T) .
Thanks
Thanh
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other
Thank you Bjoern,
I figured it out. Just use Fastx nucleotide exchanger.in Fastx-toolkit
Thanh
On Sun, Sep 22, 2013 at 4:51 AM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Thanh,
under FASTA manipulation I have one tool das is called RNA/DNA
converter. If it is not
Hi all,
I am analyzing my small RNA sequencing data on mouse tissue. Does anyone
know where to download annotation file for non-coding RNA?
Thanks
Thanh
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other
Hi,
I have been mapping my RNA-seq data to mouse genome from a different mouse
strain using TopHat. I am wondering whether TopHat can take SNPs into
account during the alignment? ( using SNPs track as an optional input)?
Thanks
Thanh
___
The
Hi Calvin,
I am analyzing miRNA differential expression from my small RNA sequencing
data from mouse tissue using Bowtie HtseqDeseq.
I tried both whole mouse genome and hairpin miRNA( from miRbase) as
reference sequences and annotation of all known miRNA (from miRbase). These
worked for me.
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