Moving average plot of gene expression ratio along the chromosome length

Question

[Susmita Mandal]

Hello,

I would like to see any chromosomal abberations in my samples and for that I want to plot moving average plots using expression values. Does anyone has any idea how to make one and what all tools I can use? Also how to find the positions of all the genes of a chromosome in humans? Any help will be appreciated.

Thanks

Susmita

[Devon Ryan]

I imagine averaging signal across samples and then making bigWigs of the ratio between each sample and that would work to show what you want. You could then just look at it in IGV. Note that it can be difficult/impossible to detect chromosomal aberrations in standard RNA-seq datasets, since it's hard to distinguish that from some other cause of gene expression changes.

[Susmita Mandal]

Can you explain this

averaging signal across samples and then making bigWigs of the ratio between each sample

[Devon Ryan]

Suppose you have samples A, B, and C. You would then make coverage tracks for each with bamCoverage or something similar then:

wiggletools mean A B C # I don't know the syntax for this off-hand, look it up

Then take the ratio of each sample to that:

bigwigCompare -b1 A.bw -b2 average.bigWig -o A_ratio.bw

[Susmita Mandal]

Will it work if I want to check the ploidy of X chromsome in my samples. It's single cell RNA -Seq.