Forum: Bioinformatics
05-20-2014, 07:54 AM
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Replies: 5
Views: 5,130
If you want enhancers on hg18, you may need to...
If you want enhancers on hg18, you may need to generate an enhancer annotation in bed format yourself.
Download the enhancer annotation from encode project, and then use liftover of UCSC to convert...
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Forum: Bioinformatics
05-13-2014, 06:50 PM
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Replies: 5
Views: 5,130
Hi trotos,
I am one of the authors of...
Hi trotos,
I am one of the authors of ngs.plot.
For the second problem, ngs.plot doesn't support enhancer annotation of hg18. You may use hg19.
For the third problem, the format of the...
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Forum: Bioinformatics
09-05-2012, 07:49 AM
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Replies: 23
Views: 40,424
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Forum: Bioinformatics
08-20-2012, 09:06 AM
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Replies: 5
Views: 10,325
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Forum: Bioinformatics
08-20-2012, 08:28 AM
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Replies: 5
Views: 1,612
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Forum: Bioinformatics
08-20-2012, 08:17 AM
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Replies: 5
Views: 2,257
http://code.google.com/p/diffreps/
I would...
http://code.google.com/p/diffreps/
I would suggest diffReps. There is a script named region_analysis.pl.
It could read bed format files and generate annotated files fitting most your demands.
The...
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Forum: Bioinformatics
08-20-2012, 08:01 AM
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Replies: 5
Views: 1,612
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Forum: Bioinformatics
08-08-2012, 08:57 AM
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Replies: 6
Views: 2,551
The quality and nature of different chip are...
The quality and nature of different chip are different, I think.
So it is alway not bad to check the coverage manually.
If you want a reliable peak list, think about IDR or MAnorm if the replicate...
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Forum: Bioinformatics
08-07-2012, 08:19 AM
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Replies: 6
Views: 2,551
Sorry I didn't explain clearly. tdf is the...
Sorry I didn't explain clearly. tdf is the coverage file format of IGV, a genome browser.
I think you'd better to generate the coverage files of chip-seq, and load them into the browser. And than...
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Forum: Bioinformatics
08-06-2012, 09:05 AM
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Replies: 6
Views: 2,551
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Forum: Bioinformatics
04-20-2012, 06:59 AM
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Replies: 13
Views: 3,277
Just curious, I googled the unique machine id:...
Just curious, I googled the unique machine id: hwi-st298.
And I found this:
http://seqanswers.com/forums/showthread.php?t=15928
It looks that the company triggered the malformation not the first...
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Forum: RNA Sequencing
06-02-2011, 07:23 PM
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Replies: 2
Views: 2,041
I think you should check the data first. ...
I think you should check the data first.
Perhaps some high abundant sequences take large proportion of the dataset.(For example, rRNA reducing failed, so some rRNA occupied many reads?)
Check the...
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Forum: Sample Prep / Library Generation
05-31-2011, 10:39 PM
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Replies: 4
Views: 5,658
Sorry, I forget the topic is about library...
Sorry, I forget the topic is about library preparation:D
Guys in our wet lab said it is hard to say the mass of total RNAs, may be 1mg? They just followed the protocols. Sometimes only when the...
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Forum: RNA Sequencing
05-31-2011, 10:08 PM
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Replies: 7
Views: 3,730
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Forum: Sample Prep / Library Generation
05-29-2011, 11:43 PM
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Replies: 4
Views: 5,658
Which species? And how about the length...
Which species? And how about the length restriction?
For what we did for human and other mammals at the length range less than 40nt, the most of final results were known miRNAs, about occupied...
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Forum: RNA Sequencing
05-19-2011, 11:28 PM
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Replies: 8
Views: 4,562
I agree with Philipp, many factors may effect...
I agree with Philipp, many factors may effect final sequencing result.
Were the datasets sequenced in same batch?
What the results of FastQC?
You may check the top 20 expressed sequences of each...
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Forum: Bioinformatics
06-17-2010, 08:10 PM
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Replies: 3
Views: 2,149
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