Mapping and alignment.
Hi there,
I'm new to RNA-sequencing. I would like to know, which is the best tool to start with for mapping and alignment of sequences. I heard of Bowtie, Tophat and Cufflinks. May I know the difference among these three and which is the best to start.
Thanks in advance
Regards, Harish Handral
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As an aside take a look at this first: A: Alignment and mapping
None of the tools you put up there are current and should not be used if you are just starting out.
STAR, HISAT2, BBMapor any splice-aware aligner would be fine followed byDESeq2/edgeR. If you are happymappingyour data thensalmon, kallistowould be your options.