How Does Tophat Work?
Hi, I see tophat use bowtie as mapping tool. But what is the difference between them.
My understand is the mapped reads in bam files that from tophat and bowtie are the same. But tophat can give junction.bed which include the junction reads, is that right?
thanks.....
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Istvan Albert
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camelbbs
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TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie.
Please read the documentation as well as the publications on this topics. This can be a good start:
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