bamtobed --> shifting --> bedtobam seems to not work with bamCoverage

[gdolsten]

Hi there, I am shifting some reads for nucleosome analysis. Currently, I use bamtobed to create a bed file, I shift this using custom scripts, then I use bedtobam to create a bam file. I sort and index, and try to pass this into bamCoverage, but I get an error: ValueError: need at least one array to concatenate

I use the following command:

bamCoverage --effectiveGenomeSize 2652783500 --normalizeUsing RPGC -b sorted.shifted_nc14.bam -o shifted.bw

Can anyone explain why I am getting this error?

[dpryan79]

Can you post the entire error back-trace?

[gdolsten]

Yeah sorry, let me try to recreate