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Forum: Bioinformatics 12-16-2014, 05:56 AM
Replies: 8
Views: 2,441
Posted By Livi81
course availability

Is the material for this course archived anyway?

Thanks in advance.
Forum: General 12-06-2013, 10:01 AM
Replies: 3
Views: 4,311
Posted By Livi81
http://opossum.cisreg.ca.

Hi,
Yes I did solve it.
I used a program developed by some local colleagues. I found it very informative and it has an easy to use interface. I hope you find it useful too.
...
Forum: General 06-17-2011, 04:42 PM
Replies: 6
Views: 2,847
Posted By Livi81
Are you analysing thousands of ChIP-Seq sites for...

Are you analysing thousands of ChIP-Seq sites for example?
I really like 'Seqpos' that can be accessed within the nice biologist friendly interface of galaxy/cistrome under the 'Motif' tools....
Forum: General 06-15-2011, 04:10 PM
Replies: 0
Views: 1,775
Posted By Livi81
TF Motif track UCSC

Hi all,

I was just thinking wouldn't it be useful to have a track option within UCSC browser showing the presence of different transcription factor motifs.
I know people have published such...
Forum: General 04-05-2011, 08:28 AM
Replies: 4
Views: 2,377
Posted By Livi81
Ok thanks for the replies, much appreciated. ...

Ok thanks for the replies, much appreciated.
I'll check out that reference.
Forum: General 04-04-2011, 07:22 PM
Replies: 4
Views: 2,377
Posted By Livi81
How reproducible is TF ChIP-Seq?

Has anyone looked at the reproducibilty of ChIP-Seq for transcription factors?
I realise that in the past expense has meant that many papers have been published without duplicates. However as costs...
Forum: General 03-30-2011, 10:53 AM
Replies: 1
Views: 1,412
Posted By Livi81
Could it be a question of biology? Is your liver...

Could it be a question of biology? Is your liver from the same sex, age, strain mouse as the published data set?
Forum: General 02-21-2011, 07:08 PM
Replies: 7
Views: 4,116
Posted By Livi81
That the protein of interest is interacting with...

That the protein of interest is interacting with the underlying DNA sequence in a given cell type or tissue.
Forum: General 02-21-2011, 05:36 PM
Replies: 7
Views: 4,116
Posted By Livi81
You're right. I guess the conclusion is that...

You're right. I guess the conclusion is that using current methods ChIP-Seq is only qualitative. It's a shame I think we're missing out on what could be interesting information.
Forum: General 02-19-2011, 07:51 AM
Replies: 7
Views: 4,116
Posted By Livi81
Hi, Sorry I should have mentioned that we've...

Hi,
Sorry I should have mentioned that we've already subtracted input control from both libraries. I was just wondering if one library has a peak of say height 20 and another library has a peak at...
Forum: General 02-18-2011, 10:13 PM
Replies: 7
Views: 4,116
Posted By Livi81
Is ChIP-Seq quantitative?

Hi all,

Can we make between library comparisons of peak height? FindPeaks was used to identify sites of transcription factor binding using the same antibody in two different cell types. If peak...
Forum: General 01-20-2011, 06:34 PM
Replies: 0
Views: 1,705
Posted By Livi81
miRNA targets expression profiles

Hi all,
I'm new to miRNA research and I'm curious about the tools already available. I have RNA-seq data from two samples, we've identified differentially expressed transcripts. I also have tag-seq...
Forum: General 10-02-2010, 12:06 AM
Replies: 0
Views: 1,989
Posted By Livi81
transfac professional

Hi,

I'm trying to get hold of the pssm for this motif V$KROX_Q6. Does anyone have access to transfac professional or know where I can find this info?

Many thanks

Livi
Forum: General 07-14-2010, 04:07 PM
Replies: 0
Views: 3,428
Posted By Livi81
'heatmap' tool

Does anyone know how I can get the 'heatmap' tool in cistrome to work?

It's under the 'annotate and visualise' subheading - it's exactly the kind of thing I need. But whatever wig file I select I...
Forum: General 07-06-2010, 10:55 AM
Replies: 2
Views: 2,277
Posted By Livi81
Hi, Thanks for the suggestion. I've since...

Hi,

Thanks for the suggestion. I've since tried uploading different files from different directories and unfortunately I get the same message.

I probably completely wrong but I think the...
Forum: General 07-05-2010, 11:29 PM
Replies: 2
Views: 2,277
Posted By Livi81
Cistrome

Hi,

I'm a bench biologist and have been using 'cistrome' for various chip seq analysis, which has been great. I was interested in integrating some previously published microarray data, however...
Forum: General 06-17-2010, 05:05 PM
Replies: 3
Views: 4,311
Posted By Livi81
Problem solved, thanks anyway!

Problem solved, thanks anyway!
Forum: General 06-16-2010, 03:05 PM
Replies: 3
Views: 4,311
Posted By Livi81
co-factor motif co-ordinates

Hi all,

I'll cut right to the chase...I want to identify regions within a chip seq data set that contain a potential co-factor motif. There seems to be lots of programs to indentify motifs within...
Forum: RNA Sequencing 05-31-2010, 10:25 AM
Replies: 26
Views: 26,797
Posted By Livi81
I'm also looking for a biologist friendly way to...

I'm also looking for a biologist friendly way to analyse RNA-seq output files. I saw that Partek seem to have some nice software, how does it compare to edgeR and DESeq?
Thanks
Forum: General 05-01-2010, 07:17 PM
Replies: 4
Views: 2,067
Posted By Livi81
Ok, great thanks for your help.

Ok, great thanks for your help.
Forum: General 04-30-2010, 05:46 PM
Replies: 4
Views: 2,067
Posted By Livi81
Transcription Factor Peaks 3' of gene

Hi,

I'm fairly new to chip seq and I've been given some transcription factor datasets to rummage through. I found some lovely peaks (consistent in 4 different samples) just beyond the 3' end of a...
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