Compute matrix skipping many regions stating not found in compute matrix output

Question

[mavy]

Hello all

I am working on Chip seq data and for generating the TSS Plots when I am computing the matrix it is giving a very long list stating "skipping NR_049895_r4, due to being absent in the computeMatrix output." and the list is very long . I tried both the bed file and the GTF file as I want to display all chromosome regions.

Any guide/suggestion on what could be the reason .

Thanks