Question: Rna Seq Data Analysis
0
gravatar for sara
5.7 years ago by
sara40
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

    bias_params.info, 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, read_groups.info, splicing.diff, tss_group_exp.diff, tss_groups.count_tracking, tss_groups.fpkm_tracking, tss_groups.read_group_tracking, var_model.info.

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

ADD COMMENTlink modified 5.7 years ago by Sudeep1.6k • written 5.7 years ago by sara40
3
gravatar for Sudeep
5.7 years ago by
Sudeep1.6k
.
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 5.7 years ago • written 5.7 years ago by Sudeep1.6k
1
gravatar for ThePresident
5.7 years ago by
ThePresident60
Canada
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 5.7 years ago • written 5.7 years ago by ThePresident60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1901 users visited in the last hour