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  • de novo Transcriptome analysis to get differential expression data

    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

  • #2
    Originally posted by nareshvasani View Post
    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?
    Last edited by super0925; 07-23-2015, 03:27 AM.

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