SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
50 bp paired end reads vs. 100 bp single end reads efoss Bioinformatics 12 01-15-2014 08:05 PM
Can Cuffdiff treat paired-end and single-end reads at the same time? zun RNA Sequencing 3 06-12-2012 05:37 PM
Can paired-end mapping produce more reads than single-end ? warrenemmett Bioinformatics 13 03-20-2012 11:10 PM
Paired-end reads mapped 50% while each pair reads mapped 80% zack80.liu Bioinformatics 3 03-03-2011 01:06 AM

Reply
 
Thread Tools
Old 09-21-2011, 07:50 PM   #1
danwiththeplan
Member
 
Location: Auckland

Join Date: Sep 2011
Posts: 72
Question paired-end reads mapped to genome.. gene with only one direction of paired-end reads?

I was hoping people would help me understand a weird situation I have encountered.

I have a genome assembly of a fungal genome (not done by me) which I have mapped raw RNAseq reads onto. RNAseq generally agrees quite well with predicted genes.

However in one gene that we are working on, the RNAseq agrees with the gene calls, but unlike other "genes" right next door on the same scaffold, all of the mapped reads are from one end of the paired end reads. The gene is big enough so that if one paired end read maps onto one end of the gene, the other one should logically be at the other end of the gene, which is the case in other genes next door.

Additionally, this weird gene has an identical copy right next door (this may be an assembly artefact)

Anyone have any idea what could cause this?

Genome assembled using velvet (I think.. not done by me) from multiple paired-end and mate-pair illumina runs.. transcriptome also from illumina runs.

Last edited by danwiththeplan; 09-21-2011 at 11:25 PM.
danwiththeplan is offline   Reply With Quote
Old 09-22-2011, 12:50 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

It sounds like an assembly artefact in the area of this gene. Maybe there is some repeat structure in this region.

If you care about it enough, perhaps a little targeted capillary sequencing could resolve it?
maubp is offline   Reply With Quote
Old 09-22-2011, 02:06 AM   #3
danwiththeplan
Member
 
Location: Auckland

Join Date: Sep 2011
Posts: 72
Default

thanks.. I am pretty sure it is a sequencing artefact on the genome, based on some wet work, but I still don't understand why only one direction of paired-end RNA reads map to these genes, but genes right next door have both directions of paired-end reads mapped to them successfully.
danwiththeplan 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 01:46 AM.


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