RNA-seq: indexing without sorting

Question

[Rakesh Tiwari]

hello there,

In RNA-seq tuxedo pipeline I was taught to directly samtools index the bam files, obtained from the tophat alignment, without indexing. and in DNA-seq I was taught that first, we sort the bam files then only index in samtools. what's the difference? and reason to do this?

thank you.

Answer 1

[WouterDeCoster]

It depends on the aligner. In this case, Tophat (as far as I know) creates a sorted bam by default. As such, there is no additional sorting necessary anymore. I believe that samtools index only works on coordinate sorted bams. By the way, TopHat is no longer a recommended aligner, and you should use something like STAR (for alignment) or salmon (for rapid pseudo-alignment).