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
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Varun Gupta
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.
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
You need to use TopHat, not bowtie, to align RNA-seq data.
Hi Sean Agreed that Tophat should be used for aligning RNA- seq data. But i guess bowtie itself is an aligner too right?
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.
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