SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 17 of 17
Search took 0.00 seconds.
Search: Posts Made By: ishmael
Forum: Bioinformatics 05-20-2014, 06:54 AM
Replies: 5
Views: 5,561
Posted By ishmael
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...
Forum: Bioinformatics 05-13-2014, 05:50 PM
Replies: 5
Views: 5,561
Posted By ishmael
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...
Forum: Bioinformatics 09-05-2012, 06:49 AM
Replies: 23
Views: 42,556
Posted By ishmael
http://www.nature.com/nbt/journal/v27/n12/full/nbt...

http://www.nature.com/nbt/journal/v27/n12/full/nbt1209-1135.html
I think this is a good start point.

PS, I am Chinese, but I don't think statistics is so simple as Chinese :-)
Forum: Bioinformatics 08-20-2012, 08:06 AM
Replies: 5
Views: 11,255
Posted By ishmael
I think BEDtools should also fit your demand. ...

I think BEDtools should also fit your demand.
1. convert the bam into bed by bam2bed
2. mergeBed.
Forum: Bioinformatics 08-20-2012, 07:28 AM
Replies: 5
Views: 1,783
Posted By ishmael
If all sequences are form human, I would suggest...

If all sequences are form human, I would suggest use reciprocal liftover approach.
1. download liftover program from UCSC.
2. download liftover chain files: both of human to gorilla and gorilla to...
Forum: Bioinformatics 08-20-2012, 07:17 AM
Replies: 5
Views: 2,409
Posted By ishmael
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...
Forum: Bioinformatics 08-20-2012, 07:01 AM
Replies: 5
Views: 1,783
Posted By ishmael
Would you mind to provide more details? What's...

Would you mind to provide more details?
What's the tool you used to do the aignment? liftover?
What's the nature of your data?
Forum: Bioinformatics 08-08-2012, 07:57 AM
Replies: 6
Views: 2,729
Posted By ishmael
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...
Forum: Bioinformatics 08-07-2012, 07:19 AM
Replies: 6
Views: 2,729
Posted By ishmael
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...
Forum: Bioinformatics 08-06-2012, 08:05 AM
Replies: 6
Views: 2,729
Posted By ishmael
I would surggest you generate the tdf file of the...

I would surggest you generate the tdf file of the coverage of genome, and load the tdf and peak lists of different p cutoff of MACS and SISSRs.
And I think the shapes of the peaks of coverage will...
Forum: Bioinformatics 04-20-2012, 05:59 AM
Replies: 13
Views: 3,666
Posted By ishmael
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...
Forum: RNA Sequencing 06-02-2011, 06:23 PM
Replies: 2
Views: 2,208
Posted By ishmael
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...
Forum: Sample Prep / Library Generation 05-31-2011, 09:39 PM
Replies: 4
Views: 6,110
Posted By ishmael
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...
Forum: RNA Sequencing 05-31-2011, 09:08 PM
Replies: 7
Views: 4,060
Posted By ishmael
For what I know, these are the contigs of genome...

For what I know, these are the contigs of genome that are not quite sure the exact position. Because there are many factors effect the assembling of genome, so some contigs the consortium didn't...
Forum: Sample Prep / Library Generation 05-29-2011, 10:43 PM
Replies: 4
Views: 6,110
Posted By ishmael
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...
Forum: RNA Sequencing 05-19-2011, 10:28 PM
Replies: 8
Views: 4,878
Posted By ishmael
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...
Forum: Bioinformatics 06-17-2010, 07:10 PM
Replies: 3
Views: 2,384
Posted By ishmael
LocaRNA is a tool based on both sequences...

LocaRNA is a tool based on both sequences alignments and secondary structures.

http://www.bioinf.uni-freiburg.de/Software/LocARNA/

You may check it.
Showing results 1 to 17 of 17

 


All times are GMT -8. The time now is 08:43 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO