generat data

[atefeh-f]

hello
I faced a problem in my implementation phase. Would you please guide me to solve it? Please find the details in bellow:
I downloaded dataset from REMC and I did run the readme file instructions on this dataset. I run this instruction:

bedtools bedtobam -i E128-H3K4me3.tagAlign -g hg19chrom.sizes > ft2.bam

but I faced with this error message :

Error: The requested genome file (hg19chrom.sizes) could not be opened. Exiting!

Thus I downloaded the file “hg19.chrom.sizes” and I run this instruction:

bedtools bedtobam -i E128-H3K4me3.tagAlign -g hg19.chrom.sizes > ft2.bam

then the error message omited. Then the above instruction produced a bam file but when I run “bedtools multicov” I faced with this error message:

bedtools multicov -bams ft2.bam -bed E128-H3K4me3.tagAlign
Could not open input BAM files.

Thus i install "samtools" and i run this instruction:

samtools sort ft2.bam > ft2.sort
samtools index ft2.sort
bedtools multicov -bams ft2.sort -bed E128-H3K4me3.tagAlign

then the error message omited.
I get RPKM from : http://egg2.wustl.edu/roadmap/data/byDataType/rna/expression/
How could I run RPKM on my files? Plus, where the instructions which I used above correct?

Best Regards