Thank you for developing and sharing this method. It has been very helpful for my analysis.
I would like to clarify one point regarding the sample1.bed file used to calculate the scale factor when generating the BigWig file.
In the example:
libSize = wc -l sample1.bed
does sample1.bed refer to the MACS2 peak file, or to a read-level BED file converted directly from the filtered BAM file?
Thank you for developing and sharing this method. It has been very helpful for my analysis.
I would like to clarify one point regarding the
sample1.bedfile used to calculate the scale factor when generating the BigWig file.In the example:
libSize = wc -l sample1.beddoes
sample1.bedrefer to the MACS2 peak file, or to a read-level BED file converted directly from the filtered BAM file?