How To Plot Rarefaction/Saturation Curve Based On Bam File Generated By Tophat?

Question

[huangqp1984]

I want to determine whether the sequencing depth is enough to cover most of the transcripts in the sample. SO, is there some tools or scripts to plot the saturation curve with the X axis being unique reads(randomly extracted in million from the BAM file generated by Tophat) mapped on genome and the Y axis being transcripts or genes detected with given uniquely aligned reads? ...thanks!

Answer 1

[Mikael Huss]

This is probably not exactly what you are looking for, but almost :-) RSeQC has a few functions to plot saturation curves from BAM files given a gene annotation. There is one for RPKM saturation (how the RPKM estimates change as a function of sequencing depth) and one for junction saturation.

Answer 2

[achamess]

Are there any readily available tools or scripts to perform this analysis? RSeqQC doesn't do it for me.

I'd like to produce a graph like this: https://cofactorgenomics.com/1-graph-will-give-you-new-perspective-sequencing-experiment/