Bowtie2 have low global alignment rates in RNA-seq

Question

[blur]

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!

[Medhat]

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

[blur]

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

[Devon Ryan]

Sounds like you should use a different analysis protocol then.

[blur]

it is taken from Nature protocols

[Devon Ryan]

So?

[WouterDeCoster]

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