What'S The Viewlimits'S Mean In Wig Format File Of Sequencing Data

Question

[Zhilong Jia]

I download 2 files. their name is as following.

mRNA_tvegetative.coverage.F.rpkm.wig : in which includes viewLimits=0:100

mRNA_tvegetative.coverage.Rpos.rpkm.wig : in which includes viewLimits=-100:0

and others like variableStep chrom=chr01 span=1 is similar.

I can not understand the F and Rpos's mean in the filename. Thank you .

Answer 1

[brentp]

The view limit tells the browser the maximum extents for the y-axis. So, from your files, it's drawing F (presumably Forward strand coverage) on above the x-axis and it's drawing the Reverse below the x-axis. This is a way to see strand-specific coverage.

[Zhilong Jia]

The filenames are strange. an F and its opposite Rpos(why not R), this is confusing. Your explain is very clear. Thank you. gotten it.

[Zhilong Jia]

By the way, I think the awk language is an amazing programming language for data process( I do love this language. it make life better). while for Bioawk, the document is just a README.bio, or is another file more detailed? Thank you very much.