SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
long ncRNA from RNA-seq stephenhart Bioinformatics 1 11-16-2012 05:32 AM
Tophat and short reads mapardo RNA Sequencing 0 09-15-2011 09:25 AM
velvet: 60bp Illimuna reads. -short or -long? Kiroro Bioinformatics 0 09-10-2011 02:10 PM
Finding Indel's and long inversions in GA data apratap Bioinformatics 3 06-17-2010 11:51 AM
Structural Variant Detection of short and long reads with NextGENe® 2nd Generation S SoftGenetics Vendor Forum 0 09-30-2009 11:32 AM

Reply
 
Thread Tools
Old 11-01-2010, 11:16 PM   #1
KevinLam
Senior Member
 
Location: SEA

Join Date: Nov 2009
Posts: 192
Default Tophat for finding long ncRNA with short reads?

Hi,
has anyone used Tophat to look at long non coding RNAs or mRNA like ncRNAs using NGS?

I am assuming of course that things would be easier if I had 454 or even Sanger reads. But Solexa and SOLiD would be more bang for the buck.

aside from de novo assembly of the transcriptome. I am wondering if it is possible to use Tophat / Cufflinks to generate the transcripts
KevinLam is offline   Reply With Quote
Old 11-02-2010, 03:12 AM   #2
natstreet
Member
 
Location: Sweden

Join Date: Nov 2009
Posts: 83
Default

I actually discovered an interesting ncRNA using the tophat-->cufflinks-->cuffcompare-->cudffdiff pipeline.

I map my reads to the reference using tophat, then run cufflinks without providing a reference gtf file. Following that I run cuffcompare where I do provide the reference gtf file and finally cuffdiff. I then screened through the significant cuffdiff results looking at the loci with no corresponding gene name entry from the reference gtf and tried to classify these. One is clearly a novel sRNA loci that has previously not been described and certainly not in the trait that my different samples come from.

So, in summary, it seems to work.
natstreet is offline   Reply With Quote
Old 11-02-2010, 05:55 AM   #3
yjhua2110
Member
 
Location: china

Join Date: Nov 2009
Posts: 49
Default grouping small rna dataset into long RNA clusters

You can try to group your small rna dataset into long RNA clusters using methods described in our deepBase ( http://deepbase.sysu.edu.cn/ ) (Yang et al. Nucleic Acids Res. 2010 Jan;38: D123-D130.).

we have identified ~1.2 million long RNA clusters by grouping all the mapped small RNA reads according to their distance in our deepBase platform ( http://deepbase.sysu.edu.cn/ ), which were developed to discover small and long ncRNAs from deep-sequencing data.

These ~1.2 million RNA clusters that include multiple classes of infrastructural ncRNAs, miRNAs precursor, piRNA precursors, repeat-associated siRNA precursors and evolutionarily conserved phastCons elements.

we have identified ~2000 microRNA candidates and ~1890 snoRNA candidates using improved miRDeep and our snoSeeker programs from these RNA clusters.
yjhua2110 is offline   Reply With Quote
Reply

Tags
assembly, ncrna, rna-seq, tophat, transcriptomics

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:51 PM.


Powered by vBulletin® Version 3.8.6
Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.