SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Try to further accelerate Bowtie2 alignment Tonnny97 Bioinformatics 1 01-17-2014 02:30 AM
Best/favorite global pairwise alignment program for proteins Khen General 0 05-06-2013 11:04 AM
bowtie2 gapped alignment Bulak Bioinformatics 0 03-11-2013 07:39 AM
bowtie2 stops during alignment moritzhess Bioinformatics 3 01-13-2013 03:53 AM
Global Alignment With Mummer (Parameter for Gap Extension & Opening Cost) peveralldubois Bioinformatics 0 03-06-2011 11:45 PM

Reply
 
Thread Tools
Old 02-17-2014, 12:19 AM   #1
Coryza
Member
 
Location: Enschede

Join Date: Feb 2014
Posts: 29
Default UTR's in Bowtie2 Global Alignment?

I've got paired-end MiSeq RNA data from Illumina, with as far as I know adapters/primers/barcodes clipped off. When mapping this data with bowtie2 against the human reference mRNA's I don't find even 1 global alignment in +- 500 sequence pairs.

Could this be due to the UTR's probably still in the sequences and not in the references? Or doesn't that matter for global alignment?
Coryza is offline   Reply With Quote
Old 02-17-2014, 12:29 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

1) You probably don't want to do that. Aligning directly against the ref mRNA will probably just make life more complicated downstream.

2) Try aligning the pairs as singletons (i.e., unpaired) and see what happens. Sometimes read #2 in a sample is complete crap and that keeps things from aligning. Also, perhaps the insert size is bigger than the default (500) or the edit distance is larger than allowed by default (i.e., tweak --score-min). UTRs should still be in the reference, it wouldn't make any sense to remove them. If they're gone, then yes, that'll seriously decrease the alignment rate, particularly in end-to-end (i.e., global) alignment.
dpryan is offline   Reply With Quote
Old 02-17-2014, 12:36 AM   #3
Coryza
Member
 
Location: Enschede

Join Date: Feb 2014
Posts: 29
Default

Why is it a bad idea to align against the ref mRNA? What should I align against too then?
Coryza is offline   Reply With Quote
Old 02-17-2014, 12:40 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

The genome. Alternatively, you could use tophat2, which will align against both in turn and only return alignments in genomic coordinates.
dpryan is offline   Reply With Quote
Old 02-17-2014, 12:43 AM   #5
Coryza
Member
 
Location: Enschede

Join Date: Feb 2014
Posts: 29
Default

Yea after bowtie2 I was planning to use tophat2. But I still don't understand why its a bad idea to don't map our mRNA data against the mRNA references.
Coryza is offline   Reply With Quote
Old 02-17-2014, 12:50 AM   #6
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

It just makes your life more complicated. Firstly, many of the transcripts will be overlapping, so when you want to determine how unique an alignment actually is then you need to recalculate everything. Secondly, the returned coordinates will be in transcript-space, which is rarely useful for anything.
dpryan 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 10:56 AM.


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