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alignment to human transcriptome with Bowtie2

I have a general question. So I see that in some publications when analyzing RNA-seq data they use Bowtie2 and human transcriptome. As I understand, Bowtie2 can not detect splice juctions, but I assume that this information is readily available in the human transcriptome. I usually use HISAT2 for RNA-seq alignment and I was wondering besides identifying alternative splicing events, Is there any advantage or difference between HISAT2 and Bowtie2+human transcriptome?

alignment
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updated by swbarnes2 swbarnes2 • written by Meghan.T • Meghan.T

1 answer

I think it's generally preferable to use a splice-aware aligner to align to the whole genome, not to use a non-splice aware aligner to align to a multi-fasta of transcripts. So I would say keep doing what you are doing.

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written by swbarnes2 swbarnes2

There are of course tools designed to give accurate transcript level counts by aligning to a file of transcripts, bowtie2 is not one of them.

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written by swbarnes2 swbarnes2

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