On Tue, Feb 22, 2011 at 2:28 AM, Jennifer Jackson wrote:
> Hi Felix,
>
> "Text Manipulation -> Convert delimiters to TAB" could split one field into
> more than one, but the delimiter has to be in the list ("@" is not).
>
> "Text Manipulation -> Cut columns" from a table is similar, but it will no
Hi Peter,
sounds nice, would be a great feature. For everyone else how is not using
a custom server: if you are lucky you can use the trim tool on tabs to
solve your problem.
If you want to add text to the beginning or end of a column:
- Use add column and add the text as a new column
- Then use
Hi,
it would be really nice if I could take a work flow and save it as a tool.
This way one could easily build custom text-manipulation tools from
already existing text tools. I already have a work flow that does a
conversion job. But it has lots of of steps that make my histories quite
messy when
On Tue, Feb 22, 2011 at 11:40 AM, Felix Hammer wrote:
> Hi,
>
> it would be really nice if I could take a work flow and save it as a tool.
> This way one could easily build custom text-manipulation tools from
> already existing text tools. I already have a work flow that does a
> conversion job. B
I've done that. The intermediate outputs are hidden.
But all the steps are still displayed. I want to hide those, too.
Felix
> On Tue, Feb 22, 2011 at 11:40 AM, Felix Hammer
> wrote:
>> Hi,
>>
>> it would be really nice if I could take a work flow and save it as a
>> tool.
>> This way one could
On Tue, Feb 22, 2011 at 1:23 PM, Felix Hammer wrote:
> I've done that. The intermediate outputs are hidden.
> But all the steps are still displayed. I want to hide those, too.
>
> Felix
I'm unclear which bit(s) you want to hide in the GUI.
With the recent enhancements, the "run workflow" dialogu
Ah, I've figured it out now :)
thx.
Felix
> I've done that. The intermediate outputs are hidden.
> But all the steps are still displayed. I want to hide those, too.
>
> Felix
>
>
>> On Tue, Feb 22, 2011 at 11:40 AM, Felix Hammer
>> wrote:
>>> Hi,
>>>
>>> it would be really nice if I could take a
Hello Christine,
The data issue goes back to the initial grooming step. When using "Fastq
Groomer", choose "Solexa" instead of "Illumina 1.3+" as the Input FASTQ
quality score type. This preserves the correct quality score
translation, which was the root of the problem in the derivative steps.
I'm a fan of viewing "coverage.wig" files - they give a nice summary of read
distribution over a chromosome.
What I like about the "coverage.wig" file is that it captures the full read
depth at every base. TDF does something different - it summarizes over
(relatively) large regions. (But this can
HI,
The option you need in IGV tools is "count". You set a window size and this
gives you a tdf file from your sorted bam (or sam) file which is nice and quick
to view on IGV.
Best Wishes,
David.
__
Dr David A. Matthews
Senior Lecturer in Virology
Room E49
Dep
David,
I have been also uisng the IGV like you have suggested.
Vasu
--- On Tue, 2/22/11, David Matthews wrote:
From: David Matthews
Subject: Re: [galaxy-user] get wig file after tophat
To: "Ying Zhang"
Cc: "Baxter, Adam" , galaxy-u...@bx.psu.edu
Date: Tuesday, February 22, 2011, 10:54 AM
Hello all,
Just a reminder that the abstract submission deadline for the Galaxy
Community Conference is next Monday, February 28. See
http://galaxy.psu.edu/gcc2011/Abstracts.html for details.
Cheers,
Dave C.
PS: And there is still space at the GMOD Meeting being held March 5-6 @
NESCent:
htt
Ying,
You can create a coverage file from a BAM file using this workflow:
http://main.g2.bx.psu.edu/u/jeremy/w/create-coverage-dataset-from-bam-dataset
While this doesn't generate a proper wiggle file, it can be a useful file for
statistical analysis.
I and others have suggested ways to visual
Hello Christine,
We have confirmed that the reads have Sanger qual format, not Illumina
(as were originally run in your history) or Solexa (as some are at NCBI,
from other SRA projects, but not this one). Please re-run the Fastq
groomer with Sanger as the input type and all should run correctl
Hi Peter,
For now we are going to recommended just using the Fastq Groomer first,
then the Clipper, to keep the tools set simple.
Apologies for the late reply, we were discussing the option internally.
Thanks for all the great ideas and contributions!
Best,
Jen
Galaxy team
On 1/6/11 4:28 A
Hi Peter,
The error when clicking tool menu links is now fixed on galaxy-central tip.
Thanks for reporting!
On Mon, Feb 21, 2011 at 4:48 AM, Peter wrote:
> > On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li wrote:
> >>
> >> All:
> >> I retested under IE7 and found the bugs you were mentioning. This
Hi Nadege,
I am forwarding your question to galaxy-u...@bx.psu.edu which is the
best place to send data questions, so that the entire team can provide
input. We will get back to you as soon as possible.
Thanks!
Jen
Galaxy team
---
Hi Jen,
I am completely new to the field of ChIP-seq and h
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