SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Dealing with super abundant transcripts in RNAseq kirby Bioinformatics 10 03-15-2013 06:12 AM
Map transcripts from de novo assemblier such as trinity back to the genome ? sptmbr Bioinformatics 5 02-29-2012 09:47 AM
"coverage" of introns, intergenic regions for RNASEQ PFS Bioinformatics 2 09-07-2011 01:51 PM
FPKM determination of de novo transcripts morebasesplease RNA Sequencing 0 08-06-2011 07:56 PM
De novo assembly of highly expressed transcripts foryvonne RNA Sequencing 12 05-04-2011 02:47 AM

Reply
 
Thread Tools
Old 07-29-2011, 07:24 AM   #1
sandmann
Junior Member
 
Location: Germany

Join Date: May 2009
Posts: 3
Default Removal of retained introns / primary transcripts from de novo RNAseq assembly

Dear all,

I have assembled a transcriptome from > 100 Mio 2x105 bp reads and obtained a nice set of sequences without a reference genome.

Some of them are very long (> 20 kb) and a blastn/blastx search revealed that they seem to correspond to transcripts that have retained intronic sequences. [I suspect that the velvet/oases assembly is most likely correct, as unprocessed transcripts are known contaminants of polyA-selected libraries. I don't have a reference genome to proof it, though.]

Still, I was wondering if anybody had any idea on how to remove such primary transcript sequences from my output before translating the sequences into putative proteins ?

Thanks for any input,
Thomas
sandmann is offline   Reply With Quote
Old 07-29-2011, 08:54 AM   #2
tboothby
Member
 
Location: DC

Join Date: May 2011
Posts: 56
Default

I am also trying to identify ways to parse out intron containing sequences from RNAseq data in an efficient way. The best way I can think of is to make contigs which include both intron containing and intron lacking variants, and then remove the intron containing transcripts from your sequence database.

Unfortunately, I am yet to find a good way to do this without a reference genome.

If you find a way to do this please let us know.

Cheers,
T
tboothby is offline   Reply With Quote
Reply

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 05:19 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO