I am a bachelor student and I am from computer science background. Recently started volunteering in a research centre.
They are doing RNA-Sequencing for human samples. I have following doubts,
From my basic research, I came to know that researchers do RNA-sequencing to study about the below 5 components.
**1) quantifying expression levels of genes, exons and splice junctions (Research articles handling this activity)
2) identifying differentially expressed genes (Research articles handling this activity)
3) discovery of gene isoforms (Research articles handling this activity)
4) mutation analysis and RNA editing (Research articles handling this activity)
5) Variant calling in differentially expressed genes and isoforms and finding CNVs and SVs (Research articles handling this activity).**
I am looking for research papers which discusses the basics of RNA-sequencing, workflows for each of the items mentioned below, tools used for each of the workflow.
For cancer and normal samples, I have fastq for each samples, tophat output files (bam), cufflinks output (transcripts files GTF) and cuffdiff output (gene_exp.diff, isoform_exp.diff,cds_exp.diff, splicing.diff, promoters.diff, fpkm tracking, raw count tracking files). With these files, how do I perform the downstream analyses for below mentioned components.