de novo Transcriptome analysis to get differential expression data

[nareshvasani]

Hello All User,

I need your help with downstream analysis. I have fastq file containing sinlge end read from ion proton instrument. I have generated de novo assembly using Trinity.
From there on wards, I am quite not sure how to get gene expression data?

Hope you guys can guide proper direction.

Thanks,
Naresh

[super0925]

Hello All User,

I need your help with downstream analysis. I have fastq file containing sinlge end reads from ion proton instrument. I have generated de novo assembly using Trinity.
From there on wards, I am quite not sure how to get gene expression data?

Hope you guys can guide proper direction.

Thanks,
Naresh

Hi Naresh
Have you done that? I want to do the similar issue which focus on DE genes analysis.
I thought after Trinity , the downstream is RSEM and DESeq , am I right?