Is This Always The Case That The Wig/Bigwig/Bed Files Are Meant Only For Viewing Into Ucsc Browser?

Question

[ashis.csedu]

Since I'm currently working with RNA-seq experiment data stored in wig/bigwig format. There are wig/bigwig files for separate experiments (after applying different stimulations). The wig files contains several million short-read information that adapts the following file format convention:

<chromosome_name> <start_coordinate> <end_coordinate> <some_score>

This wig files are already aligned with the reference genome and their bigwig counterparts are meant to be viewed in UCSC genome browser, right?

As bioinformatics point of view, what does the UCSC genome browser provides to us? is it only the manual viewing, or something else that we can extract meaningful?

What additional tools (or software) can I apply to work with this wig/bigwig files? Thanks.

Answer 1

[Pierre Lindenbaum]

no bigwig/bigbed is just a format that can be used to handle your personnal data on the client side. You can use an API a incoporate it into YOUR programs. There is a C API available from the UCSC and a java API ( http://code.google.com/p/bigwig/) . The UCSC also provides some standalone tools to handle the big* files on the client side : http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

[ashis.csedu]

Thanks for the information.