RNA seq workflow

Question

[bioinfo]

I'm currently doing analysis for RNA-seq Here's my question my Experimental condition media A biological replicates media B biological replicates

As a result, I have 4 NGS outputs containing paired end reads : mediaA1(R1,R2) mediaA2(R1,R2) mediaB1(R1,R2) mediaB2(R1,R2)

my understanding of workflow was TopHat->cufflinks(doing each sample)->cuffmerge(merge transcriptome mediaA1,2 & B1,2) -> cuffidff

I don't know if it's what I understand. Thank you

[GenoMax]

Please consider this: C: Trouble using TopHat (bowtie index genome.*.bt2l)

Answer 1

[johnsenkyle13]

I don't know if there's newer stuff out there (that's what I'm looking for now), but there are for sure newer, better programs than the ones you mention. There's HISAT2, StringTie, and Ballgown for example.