Is bowtie fit for 90 bp reads?

[bluelotus]

Hi,all,
I'm new to next-generation sequencing,and I have a data set of paired-end reads of length 90 bp.I used bowtie to map the reads into the reference genome,but the result is not good.
Could anyone tell me if bowtie is fit for processing the 90 bp reads?Maybe I'll work with TopHat,but it seems to use bowtie to map reads and not works with bowtie2.
A lot of thanks.

[andreas.sjodin]

Bowtie 1 and 2 works well for mapping 90 bp reads. For the difference between version 1 and 2, please consult this section in the manual

[arvid]

If it is RNA-derived reads, you should use TopHat when mapping to the genome, since bowtie alone won't splice-align the reads...

[andreas.sjodin]

Agree, of some reason, I assumed it was not rna-seq reads that were mapped...

[bluelotus]

If it is RNA-derived reads, you should use TopHat when mapping to the genome, since bowtie alone won't splice-align the reads...

Thank u ,I'll give it a try.

[bluelotus]

Agree, of some reason, I assumed it was not rna-seq reads that were mapped...

Thank you for your answer.These reads are RNA-seq reads of a kind of fungi.Maybe I should learn more about bowtie and tophat.