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 :)