Question: RNA seq workflow
gravatar for bioinfo
16 months ago by
bioinfo10 wrote:

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

rna-seq • 556 views
ADD COMMENTlink modified 16 months ago by johnsenkyle130 • written 16 months ago by bioinfo10

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

ADD REPLYlink written 16 months ago by genomax67k
gravatar for johnsenkyle13
16 months ago by
johnsenkyle130 wrote:

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.

ADD COMMENTlink written 16 months ago by johnsenkyle130
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