Discrepancy between bigwigs generated by bedtools and deeptools

[Caffeinated-Code]

Description of the bug

Two sets of bigWig coverage graphs are generated using bedtools and deeptools in v2.1.1.
The deeptools bigWig looks accurate and captures the bidirectional strand-specific signatures (green track).
But, the bedtools bigWigs on both strands are almost mirror images (brown track) - strand-specificity is lost (brown track).

Deeptools addresses and handles this strand-specificity issue:
Deeptools BamCoverage
Biostars Discussion

UCSC Browser/IGV visualization of these bidirectional transcriptional signatures from deeptools is helpful in guessing transcriptional start sites that can also be confirmed with PINTS/dREG peak calls.
In order to avoid confusion, future pipeline versions can drop generating bedtools coverage graphs.

Command used and terminal output

# Bedtools command run by nascent pipeline
bedtools genomecov -ibam sample.umi_dedup.sorted.bam -bg -strand + > sample.plus.bedGraph

# Deeptools command run by nascent pipeline
bamCoverage --bam sample.umi_dedup.sorted.bam --filterRNAstrand forward --numberOfProcessors 2 --outFileName sample.plus.bigWig

# Deeptools also generates bedgraphs if needed with this option
--outFileFormat bedgraph

Relevant files

System information

Nextflow Version: 23.04.1
Hardware: AWS Cloud9
Executor: Local
Container engine: Docker
OS: cpe:2.3:o:amazon:amazon_linux:2
Nascent Pipeline Version: v2.1.1