During development of a pipeline involving Genrich for integrating ATAC seq with ChIP-Seq for multiple marks, I wish to only call peaks on a few small regions. For this reason, it is desirable to be able to specify which chromosomes or bed-regions to include.
The effective genome should then be the regions to include minus the regions to exclude.
This would allow me to tell Genrich to analyze, eg, chr8 only, minus any pre-computed global region black-list.
Finally, being able to specify chromosome to include or exclude using regular expression would be great. One useful expression would be `-i ^chr\d+$' to effectively remove (in the case of exnsembl zebrafish) chrM and an of the "unknown" chromosomal fragments matching "chrUn_*".
This feature would also simplify life for people seeking an easier way to #29.
During development of a pipeline involving Genrich for integrating ATAC seq with ChIP-Seq for multiple marks, I wish to only call peaks on a few small regions. For this reason, it is desirable to be able to specify which chromosomes or bed-regions to include.
The effective genome should then be the regions to include minus the regions to exclude.
This would allow me to tell Genrich to analyze, eg, chr8 only, minus any pre-computed global region black-list.
Finally, being able to specify chromosome to include or exclude using regular expression would be great. One useful expression would be `-i ^chr\d+$' to effectively remove (in the case of exnsembl zebrafish) chrM and an of the "unknown" chromosomal fragments matching "chrUn_*".
This feature would also simplify life for people seeking an easier way to #29.