I have downloaded DGE tag reads from NCBI SRA, I need to know how to align, assemble and annotate the DGE tags. I have used tophat and cufflinks but it is not working. Kindly help me in this regard................
Can you be more specific about these "DGE Tags"? I think that the definition is really vague, for example see:
https://www.biostars.org/p/197943/
If this is RNA-seq data, then you can use automated pipelines to avoid learning everything. You can use for example some pipelines on Galaxy servers.
Otherwise I would recommend to read the article these data come from (how did they analyse the data), follow the reads treatment from the article (triming of the adaptors, etc), map the reads from the FASTQ files to the reference genome with STAR, use FeatureCounts to count the reads per gene, and then follow the steps described in this paper for differentially expressed genes analysis (in R, the scripts are provided):