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 Galaxy User list should be used for the discu
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
Hi,
I have illumina ChipSeq data in txt format with this structure:
@HWI-EAS225:8:1:1:58#0/1
NAGAGTGCCCGGGTTCAGTTCTCAGCACCCATGTGG
+HWI-EAS225:8:1:1:58#0/1
DMSSUSSTTTUTSRQRTTTSSSUS
@HWI-EAS225:8:1:1:1803#0/1
NCCATGGGAAGAGCTGGGCAGGCGGGCCGAGCGAAG
+HWI-EAS225:8:1:1:1803#0/1
DLSTTSKOUTRRTTS
Does anyone know what happened to the chip-seq exercise by James?
It was part of a collection here:
http://main.g2.bx.psu.edu/u/james/p/exercises
and it was linked here:
http://main.g2.bx.psu.edu/u/james/p/exercise-chip-seq
But is it 'Not Found'.
It was a very useful exercise. Will it be back
Giuseppe,
Your ChipSeq data is already in fastq format. It appears to have Illunima
quality scores, so you'll need to use the NGS:QC and manipulation > FASTQ
Groomer tool, using 'Illumina 1.3+' as input and 'Sanger' quality format
as output.
As to using MACS, I've never used it before but you shoul
Hi Josh,
Thank you for reporting this issue, it has been resolved. Please let us know if
you encounter additional problems in the future.
Thanks for using Galaxy,
Dan
On Mar 21, 2012, at 8:18 PM, Joshua Udall wrote:
> Does anyone know what happened to the chip-seq exercise by James?
>
> It
Hi Dan -
I agree this tutorial is very helpful. In running through this exercise
recently, however, I noticed a few very small things that could help improve
this already excellent tutorial for new users:
1) you may want to explicitly tell people to create an account first if they
haven't so
Jen,
I ran the flow as you suggested, but got following error message, Do You hav
eany suggestion? I added 0 and flips the columns: Here is the few lines of
input file:
chr1
12137
12336
61R33AAXX100706:1:79:7707:9270
0
-
chr1
31542
31741
61R33AAXX100706:1:37:11341:10600
1
-
chr1
39921
401
Hello Vasu,
The score value should be "0" for each row. When adding the new column,
set "Iterate?:" to the default "no".
It also looks like there may be some inconsistencies in the original
file. Are you certain it is 5 columns (exactly) for every row? Including
the error row reported? Some
Hello,
My name is Christopher Terranova and am a M.S student at the University of
Buffalo SUNY.I have been attempting to analyze my MACS data using Galaxy,
already
have my custom peaks on the UCSC Genome browser and have some specific
questions.
I am attempting to show how my peaks (and peak cen
Hi everybody.
I´m trying to analyze Chip-SEq Data from Ion-Torrent using Peak Calling/MACS. I
have some questions:
· How do I establish the Tag size? The median of size reads in my data
are 156pb, the max 306?
· Bandwidht: is the sonication size?
Thanks in advance
Regards
☺
Hi everyone,
I have a list of genomic regions with some variants and would like to study
the correlation between theses variants and epigenomics marks such as
histone modifications.
>From Encode download page, i got some files corresponding to peaks of these
hsitone modifications and would like t
Hello Mónica,
The median size is probably fine, unless the distribution of size is
highly skewed or dispersed, but even then you have to start somewhere. I
have always thought this post on the MACS google group was good advice.
With short tags, original read seemed to map in entirety most of t
Hello Rad,
Dan will be able to help you get started and build up a workflow for
your analysis. He is currently on vacation, but will be returning soon
and will contact you directly when he returns.
We are very sorry about the delayed reply. Please know that we
definitely want to help you to
Please keep me on the loop as I am also interested in similar workflow.
Many thanks and best regards,
Jorge
On Thu, Jun 23, 2011 at 3:21 AM, Jennifer Jackson wrote:
> Hello Rad,
>
> Dan will be able to help you get started and build up a workflow for your
> analysis. He is currently on vacation,
Thanks Jennifer
Rad
2011/6/23 Jorge Andrade
> Please keep me on the loop as I am also interested in similar workflow.
> Many thanks and best regards,
> Jorge
>
>
> On Thu, Jun 23, 2011 at 3:21 AM, Jennifer Jackson wrote:
>
>> Hello Rad,
>>
>> Dan will be able to help you get started and build
Hi Rad, Jorge,
Sorry for the delay in reply. We have not yet released a pre-canned workflow
to do this. However, if you are looking to associate one set of Genomic
interval/region data with another set, Galaxy's interval operation tools are a
good place to begin. There are good examples of usi
Dear Galaxy,
I am trying to analyze my ChIP-Seq data from Illumina using Galaxy. I have 2
datasets that I want to compare after normalizing each of them to their
respective inputs, and these 2 datasets have very different number of reads to
start with, is there a way to first normalize each dat
Hi Catheryn,
for ChIP-seq analysis, normalisation and BAM file correlation we use
deeptTools. Here you can read more about it:
https://github.com/fidelram/deepTools
And here is the toolshed repository:
http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools
Cheers,
Bjoern
> Dear Galaxy,
>
>
19 matches
Mail list logo
