RNA-seq differential expression analysis at specific defined intervals (downstream 1kb adjacent region to repetitive elements)

Question

[jennxyzhang]

I have aligned RNA-seq samples in triplicate for two conditions from a colleague (*.BAM files).

I want to examine the log2fc of condition1/condition2 in defined 1kb regions that I have annotated a .BED file for the genome build I am working with (hg19).

Strategies I am thinking about:

• bedtools intersect to narrow down the aligned reads (.BAM files) to just the ones aligning to the defined regions of interest (.BED file) --> Deeptools bamCompare to calculate log2fc(condition1/condition2)--> Deeptools computeMatrix and plotheatmap

• featureCounts with SAF annotation using the annot.ext argument to define regions of interest then proceeding with countToFPKM to calculate FPKM and then plotting differentially expressed regions in a heatmap

I'm a total novice in RNA-seq analysis, so any feedback/suggestions from experienced bioinformaticians is deeply appreciated! Thank you :)