Bowtie1 Gapped Alignment

Question

[Varun Gupta]

Hi Everyone

I used bowtie1 for RNA seq dataset. Now bowtie1 manual says that it does not support gapped alignment. So does it also mean that it will not report any alignments with N in the cigar string i.e. the spliced alignments.

Moreover what role does bowtie1 plays in Tophat. Is it just the indexing of the ref genome or something else also.

Hope to hear from you guys soon

Varun

Answer 1

[Sean Davis]

Bowtie1, if used in TopHat, will produce the N in the cigar string just fine. However, if there is a small exonic insertion or deletion in the sample, reads that cover that indel will not be aligned using bowtie1. So, the "gap" in TopHat that is not supported is the small indel, not the intron.

[Varun Gupta]

So Sean It means if i am using only bowtie1 to align short reads of around 32 bp, i will not get N in the cigar string of the sam file produced from bowtie1 mainly because reads are smaller in length

But if i am using bowtie1 with long reads such as 75bp will i get N in the cigar string or no

[Sean Davis]

You need to use TopHat, not bowtie, to align RNA-seq data.

[Varun Gupta]

Hi Sean Agreed that Tophat should be used for aligning RNA- seq data. But i guess bowtie itself is an aligner too right?

[Sean Davis]

Bowtie is used by TopHat to do RNA-seq alignment. You should really consider reading the TopHat paper if you are going to be using that algorithm.