All of us, at least people working on NGS data analysis, are familiar with these three data types, and we are refering to UCSC documentation to understand their content and meaning. That's nice, but still there is some black boxes not necessary clear especially these questions :
- how comes that these files generated for the same experiment by different programs, create different values and different distribution
- a question that is more related to these programs now, how are these files created from reads alignments ? What algorithm is behind these files ?
- documentation on the format are clear enough, but significance and meaning of the scores inside each file are not explained, what are these values referring to ?
- look at this sentence from UCSC " The BedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data" : probability score ? Of what ? How ?
I hope i am not merging a lot of questions in a single post, they are all related and i think it is worth mentionning them in block so that we can discuss them in the same time.
Thanks for all.