I have RNA-Seq data from different stages of a parasite and I am investigating only certain genome areas. I have already done a Deseq analysis and some of the genes are differentially expressed. Now I have merged the mapped reads to get the elongated reads, to get the whole RNA fragments. These RNAs are of different lengths in the different stages (sometimes just 5 bp difference). There are always several reads mapped (different RNAs) on a region that I am investigating. I wanted to graphically display the regions where the RNA is mapped to the genome sequence with the different stages among each other. It could look like the Graphic Summary of BLAST, where the reference genome is first, and than the shorter pieces below.
My first idea is to make a local alignment to get the "blocks" where the sequences map to the reference sequence, but I have no idea how to get a visualization of an alignment. I have the mapped reads a bam files or the extracted RNAs as fasta files. I hope you can help me.
Have you checked out Integrated Genome Viewer (IGV) from Broad Institute? If you have BAM alignments then this would be one way to visualize.