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?