Using Tophat2 to align illumina files to ucsc hg19

Question

[fk566938]

Hello, I need to use Tophat2 to align RNAseq from 16 tissues (downloaded from the European Nucleotide Archive part of the illumina body map project) to UCSC genome browser's hg19. I have the .fa file for the hg19. I think Tophat2's output files are bam files. I don't know the command to do this alignment. I am a bench scientist and not so much a bioinformatician. Does anyone know the command?

Answer 1

[h.mon]

First, the authors of TopHat are retiring it, you should use HISAT2 instead:

• HISAT2 is a successor to both HISAT and TopHat2. We recommend that the HISAT and TopHat2 users switch to HISAT2.

Second, I have used Subread and in addition to being very good, it has a very easy to follow users guide. The "quick start" on page 13 will get you on to mapping in no time, and after you start mapping, just read the rest of the guide to learn what you are doing.