On Jun 10, 2011, at 7:10 PM, Joanne Rampersad wrote:
> Hi
> Is there an stand alone ( ie not a component of Bowtie etc ) program
> in galaxy that can filter or trim fastq data?
its under NGS TOOLBOX BETA
NGS: QC and manipulation
best,
ido
___
On Jul 10, 2011, at 8:00 AM, YOGESH OSTWAL wrote:
>
> Dear Galaxy users,
>
> This is Yogesh, a new galaxy user, very new to programming as well. Can
> anybody guide me from where to start to learn ChIP-Seq analysis?
Maybe with galaxy you don't have to program.
Its difficult to help you without
On Jul 11, 2011, at 10:04 AM, YOGESH OSTWAL wrote:
> thanks a lot.
>
> Sorry for disturbing you again.
>
> Before starting with the actual data, can I try this analysis with already
> available IP and input files of datasets of illumina from NGS repository?
why shouldn't you?
select something
On Aug 3, 2011, at 12:49 AM, Addwebi, Tarek wrote:
> Hi Dear
> Is there anybody whom I can share my data with? I have an important question
> that I tried to answer, but I could not. Please see the attachment first,
> and let us see the first read in the first row. I need to know how many time
On Sep 21, 2011, at 8:47 AM, shamsher jagat wrote:
> Can I analyze two bed files from Chip seq experiemnt in Galaxy? I have one
> file of input and other of sample. Both these files have peak locations. Any
> suggestion of a work flow in Galaxy?
>
>
The bed file consists of called peaks don
I think what you want is "Collapse sequences" in the Fasta manipulation tab.
HTH,
ido
forgot the list CC.
On Jan 11, 2012, at 5:36 PM, Florian Peschke wrote:
> Hi there,
>
> I am not quite sure if Galaxy can help me but I am looking for way to
> transform a fastq file into Unique Seuqence ta
On Nov 20, 2012, at 11:21 AM, Kevin Y wrote:
> Hello,
> Is there a way to get unmapped reads from tophat?
Only the very latest tophat version 1.4.1 IIRC (and maybe tophat2 from the
beginning) save unmapped reads into a fastq.gz file output,
and its not an option.
I don't think the galaxy output
Hi,
is it possible to do a conditional in the compute tool?
something like:
"a" if c1 == 4 else "b"
or
if c1 == 4 "a" else "b"
or
c1 == 4 ? "a" else "b"
thank you very much,
ido
___
The Galaxy User list should be used for the discussion
Is there now a better way to import files that are actually already in galaxy?
Is there a trello card for this?
It would save our users a lot of time and nerves to be able to do this.
thank you very much,
ido
On Mar 21, 2013, at 6:01 AM, Jennifer Jackson wrote:
> Hi Ann,
>
> For just using
Not all the files should be converted to datasets. It would be good if there is
a restful API call for this saying "promote this
output file to a dataset in the background". Then one could create HTML pages
with many output files without cluttering
the history and the user can herself decide whic
You could use the adaptor clip with e.g. a custom poly-A 'adaptor'
its in FASTX-Toolkit for FASTQ data
best,
ido
On Jul 28, 2013, at 8:44 PM, Larry Simpson wrote:
>
> Hi
>
> Is it possible to trim a variable number of a specific nucleotide from the 3'
> ends of fastq RNA reads? The "Manipula
You should add 10 lines from one of your files.
Then its easier to understand the problem.
best,
ido
On Aug 26, 2013, at 5:17 PM, "Law, Michael J." wrote:
> Hello,
> I am completely new to using galaxy. I have a quick question. I have uploaded
> my fastq files generated from my experiment for
I have a login
> (clearly since I have used ftp for data upload). How do I fix this?
> Thanks so much,
> Mike
>
> Michael Law
> la...@rowan.edu
>
>
>
> On Aug 27, 2013, at 4:44 AM, Ido Tamir wrote:
>
>> You should add 10 lines from one of your files.
&
Please be more specific about which quality of what gets reported.
Why do you think its important to reduce the difference between mean and median?
best,
ido
On Nov 6, 2013, at 4:50 PM, Benjamin Osei-agyeman
wrote:
> Hi,
> After obtaining a quality report in galaxy I found out that there is a
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