Find intervals where the mean RNA-seq coverage among 3 (for example) samples is >= a minimum threshold.

go.sh

# compute a BEDGRAPH RNA-seq coverage across the entire genome for each sample:
bedtools genomecov -bga -split -ibam sample1.sorted.bam > 1.bg
bedtools genomecov -bga -split -ibam sample1.sorted.bam > 2.bg
bedtools genomecov -bga -split -ibam sample1.sorted.bam > 3.bg


# compute the mean coverage at each interval.
bedtools unionbedg -i 1.bg 2.bg 3.bg \
   | awk '{sum=0; for (col=4; col<=NF; col++) sum += $col; print $0"\t"sum/(NF-4+1); }'
chr1 900  1000 0  60 0	20
chr1 1000 1500 10 60 0	23.3333
chr1 1500 1600 0  60 0	20
chr1 1700 1980 0  50 0	16.6667
chr1 1980 2000 0  50 80	43.3333
chr1 2000 2050 20 50 80	50
chr1 2050 2070 20 0  80	33.3333
chr1 2070 2090 20 0  0	6.66667
chr1 2090 2100 20 0  20	13.3333

# filter such that intervals must exceed a minimum mean coverage (e.g., 10) among the samples:
bedtools unionbedg -i 1.bg 2.bg 3.bg \
   | awk '{sum=0; for (col=4; col<=NF; col++) sum += $col; print $0"\t"sum/(NF-4+1); }' \
   | awk '$7 > 10'
chr1 900  1000 0  60 0	20
chr1 1000 1500 10 60 0	23.3333
chr1 1500 1600 0  60 0	20
chr1 1700 1980 0  50 0	16.6667
chr1 1980 2000 0  50 80	43.3333
chr1 2000 2050 20 50 80	50
chr1 2050 2070 20 0  80	33.3333
chr1 2090 2100 20 0  20	13.3333