RNA-seq experiments with TopHat2

Question

[Sam]

I’m using this code for my trimmed paired-end RNA-Seq libraries

tophat2 -o outdir --mate-inner-dist 60 --mate-std-dev 50 -p 6 --GTF <annotation_file.gtf> -g 2 --library-type fr-secondstrand --no-discordant --no-mixed <bowtie2_index> file_trimmed_1.fastq file_trimmed_2.fastq

and prepare the count table with featuresCount from bam file for differential expression analysis.

Is it a correct way?

Thanks

Answer 1

[WouterDeCoster]

Unless you have good reasons to do so, you should run most tools with default parameters. In addition, you should also know that TopHat is in low maintenance and considered deprecated. It still works, but it's not considered the state of the art spliced aligner anymore. For that, have a look at HISAT2 or STAR.