projecting short reads on the transcript

Question

[ashkan]

Hi

I am going to project short reads (from sequencing) on the transcriptome. does anyone know how I can do that. my final goal is to get the density of reads from start to stop codons.

thatnks

[GenoMax]

If you are aligning reads then in a way you are doing that already. If projection means visual display then a genome browser tool like IGV would be appropriate. An interval file and a package like featureCounts would allow you to get "density" (# reads) at any position.