Question: Bowtie2 have low global alignment rates in RNA-seq
0
gravatar for blur
2.4 years ago by
blur90
European Union
blur90 wrote:

Hi,

I have been running bowtie2 on RNA seq and eCLIP data a lot lately, and when I use the default global alignment option I get at best 45% of the reads aligned. The rates are better using local aignment, Is this a normal alignment rate? I used to run bowtie on DNA all the time and the rates were about 95%. Should I trust these results? Is it OK to use local alignm,ents instead?

Thanks!

eclip bowtie2 • 760 views
ADD COMMENTlink written 2.4 years ago by blur90
1

why you don't use SOAP-splice, STAR or tophat (HISAT2 is alternative now)? splice-aware mapping is preferred.
In case of DNA "genomic" alignment sure Bowite will give you good result cause there is no splicing here

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Medhat8.2k

I am following a specific protocol that entails bowtie2 (I use STAR for other anylises)

ADD REPLYlink written 2.4 years ago by blur90

Sounds like you should use a different analysis protocol then.

ADD REPLYlink written 2.4 years ago by Devon Ryan88k

it is taken from Nature protocols

ADD REPLYlink written 2.4 years ago by blur90

So?

ADD REPLYlink written 2.4 years ago by Devon Ryan88k

That doesn't necessarily make it appropriate for this analysis. Which organism do you work on? Try to be as informative as possible.

ADD REPLYlink written 2.4 years ago by WouterDeCoster37k
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