Change window size in wiggle file.

Question

[tsomakiank]

Hi there! I got some bedgraph files from macs2 and converted them to wiggle and bigwig using scripts from UCSC. As far as I can understand changing the window size or binning is a way of lowering the resolution of the peaks from 1 bp to peaks coming from a sum of larger regions (correct me if I am wrong). My question is how i can change the window size of my files. Thanks in advance.

Answer 1

[Marco Pannone]

Yes correct, your defined bin size will indicate how many adjacent bases will be averaged in one single value when producing your coverage file.

To my knowledge, the only way you can change the bin size is when you produce the coverage file (.bigWig format, for example) starting from a .bam file. This can be easily done tuning the --binSize argument in bamCoverage.

If you do not have access to the .bam files, I do not think you can do that. You can't generate the .bam files starting from a coverage file.

[tsomakiank]

Thanks for replying Marco. Is there any way I can do that to peak file formats and not read alignments?

[Marco Pannone]

No, you need the .bam files, unfortunately.

[tsomakiank]

Oook, got it! Thanks for the help Marco!