Mapping and alignment.

Question

[harishkiran.handral]

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

[GenoMax]

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, BBMap or any splice-aware aligner would be fine followed by DESeq2/edgeR. If you are happy mapping your data then salmon, kallisto would be your options.