Question: Rna Seq Data Analysis
gravatar for sara
6.5 years ago by
sara40 wrote:

Hi all!!!

I am new to analysis the RNA-seq data.

As far now i used bowtie for indexing the reference genome, picard to find mate-inner-distance, tophat for aligning our reads to the reference genome, cufflink to get GTF file of transcript, cuffmerge to merge the transcript file of both diseased and normal, And then i did cuffdiff to get differention expression data.

Now am having, cds.count_tracking, cds.diff, cds.fpkm_tracking, cds.read_group_tracking, cds_exp.diff, gene_exp.diff, genes.count_tracking, genes.fpkm_tracking, genes.read_group_tracking, isoform_exp.diff, isoforms.count_tracking, isoforms.fpkm_tracking, isoforms.read_group_tracking, promoters.diff,, splicing.diff, tss_group_exp.diff, tss_groups.count_tracking, tss_groups.fpkm_tracking, tss_groups.read_group_tracking,

These are the files i got in after running cuffdiff. Can anyone help me on hoe to proceed further?

ADD COMMENTlink modified 6.5 years ago by Sudeep1.6k • written 6.5 years ago by sara40
gravatar for Sudeep
6.5 years ago by
Sudeep1.6k wrote:

Before going in any direction, I would recommend to go through some of the previous Biostar threads like Rna-Seq Review Papers, Survey: Rna-Seq Analysis For Differential Gene/Transcript Expression [Updated With Results] and Rna-Seq Data Analysis & Good Review/Research Article On Same. The links in those threads will give you an idea on a number of analysis methods and also an initial idea on how to play around with your data.

ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by Sudeep1.6k
gravatar for ThePresident
6.5 years ago by
ThePresident60 wrote:

The file called "gene_exp.diff" will contain everything you need for differential expression (including statistical parameters). You might begin with that file to asses you DE genes.

edit: you can use "genes.fpkm_tracking" to get your FPKM values which can be useful to compare genes expression within a single library.

ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by ThePresident60
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