Hi, Yan
The htseq_bams_to_count_matrix tool in the test toolshed might be worth a
try - it creates tabular count matrices from any number of individual
sample bam/sam files (it is NOT read group aware!). Each row contains the
count for that contig for each sample. It uses HTSeq code and you
Hi Yan,
You may use the HTseq count wrapper in the http://galaxy.nbic.nl/.
It does a good job and I could employ edgeR on that count matrix.
Good luck.
Best wishes,
Anto
___
The Galaxy User list should be used for the discussion of
Galaxy
Hi Anto,
Thank you very much for your reply! I tried Galaxy/NBIC. However, I had
problem with uploading my files. I used FTP, because the file I had was
larger than 2G, but I couldn’t connect to the NBIC FTP. Do you have some
idea how to solve the problem? Thanks!
Yan
发件人: Anto Praveen
Hi Yan,
I also had problems with NBIC FTP.
NBIC allows only 10 GB space for user.
I made my BAM files in main server (using Tophat2) and then uploaded them to
NBIC using their download URLs.
It was fast. It took me less than a hour to move 16 BAM files (around 9.5 GB).
You may try this.
Good
Hi Anto,
Thanks so much! I will try.
Best wishes,
Yan
发件人: Anto Praveen Rajkumar Rajamani [mailto:a...@hum-gen.au.dk]
发送时间: Thursday, August 22, 2013 3:57 PM
收件人: Yan He; galaxy-user@lists.bx.psu.edu
主题: RE: [galaxy-user] Counts of mapped reads for each gene?
Hi Yan,
I also
On Thu, Aug 22, 2013 at 12:07 AM, Ketan Maheshwari
ketancmaheshw...@gmail.com wrote:
Hi,
I am wondering if it is possible in Galaxy to design a tool whose sole
purpose is to run other tools.
This is motivated by our desire to enhance execution capabilities of
existing tools via a generic
Hi,
I am wondering why Cuffdiff suddenly gives many more significant DE genes?
I have used same input data and now get approx 5x more significant genes,
settings is same with the exception that you now included library normalization
and dispersion estimation. See below for parameters.
I have
Hello John,
Use Make windows with the sliding window option (for example, offset
=1), then use Text Manipulation - Select random lines.
Best,
Jen
Galaxy team
On 8/22/13 7:06 AM, 师云 wrote:
Dear Galaxy develop team:
As the subject said, I need to obtain random regions which are
1000-bb,
Hi,
I was using the clip program, but my adapters are on the 5' end. Is there any
way to use this program so it will clip the 5' end or a way to make all my
reads the reverse complement and run it through this program?
Thanks
___
The
Hello,
The Clip program only acts on the 3' end. In some cases, running
FastQC to isolate adapter regions, then using a tool like FASTQ
Trimmer or Trim will work (if the lengths are somewhat fixed).
Alternately, the tools NGS: QC and manipulation - Reverse-Complement
or Manipulate FASTQ
Hi Jen,
Thank you very much!
Best,
John
From: Jennifer Jackson
Sent: Friday, August 23, 2013 12:21 AM
To: 师云
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] How to get random region of 1000-bp window in the
chromosome not overlapping specific [gtf] file
Hello John,
Use Make
Hello,
This Galaxy wrapper is based on the FASTX-Toolkit tool by the same name.
A link to the original is at the bottom of the tool's form in the UI. To
see the Galaxy wrapper, it is in the source here: galaxy-central / tools
/ fastx_toolkit
https://bitbucket.org/galaxy/galaxy-central
Hi Jen and other Galaxy-users,
I am working on exome-capture sequencing with NGS. I am wondering if there
is a tool to identify SNPs on Galaxy? I would like to get SNP information
(position and allele frequency ) for each gene. Any information is highly
appreciated! Thanks!
Best wishes,
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