nf-core
Change bigWig creating to use `--bga` option
Description of the bug
We have observed an interesting behaviour when it comes to the bigWig file generation in both the ChIP-seq as well as CUT&RUN workflow, and I wanted to open this up to your collective input.
The ChIP-seq pipeline runs the following code to generate bigWig files:
bedtools genomecov \
-ibam H3K27me3.mLb.clN.sorted.bam \
-bg \
-scale $SCALE_FACTOR \
-pc \
| sort -T '.' -k1,1 -k2,2n > H3K27me3.bedGraph
This default behaviour creates bigWig files that appear to have a relatively high level of background. When using the option --bga (instead of --bg), uncovered bins get assigned values of 0 and are not skipped. This appears to result to lower levels of background, which is more pleasing to the eye in IGV:
I have just discussed this with @FloWuenne and @edmundmiller during the weekly helpdesk, and they agreed that this behaviour should be changed (@JoseEspinosa for visibility).
Very detailed additional findings, inclduing IGV screenshots etc, are availalbe on the nf-core Slack: https://nfcore.slack.com/archives/CFP55NZ5G/p1747062371347069
The current ChIP-seq workflow seems to use this local code: https://github.com/nf-core/chipseq/blob/51eba00b32885c4d0bec60db3cb0a45eb61e34c5/modules/local/bedtools_genomecov.nf#L30
But ideally BEDTOOLS_GENOMECOV should be changed over to using the nf-core module, together with changing the -bg to --bga. Users still wishing to specify--bg could do so via the ext.args parameter.
Command used and terminal output
Relevant files
No response
System information
No response
An alternative solution to simply changing the parameter hardcoded in the module could be to replace the local module with the nf-core module, provide these additional flags via ext.args and thereby allowing end-users to chose which parameter they want. This would maintain functionality across new releases but provide the option to modify behaviour for users going forward: https://github.com/nf-core/chipseq/issues/469
