Dear biostar users,
I would like to detect aneuploidy between samples - I have reference (healthy sample) and aneuploidy samples...
After run my workflow I have on output:
bins no_reads GC_content
So I have each chromosome split into the bins and calculated in each bins number of reads and cg_content for each bin. Do you have any idea how to normalize number of reads to apply some statistical test for comparing data to each other?
I was thinking to apply analysis from RNA-seq data - sequencing depth (RPGC) = (total number of mapped reads * fragment length) / effective genome size (analogy to RPKM) - but it is not probably good idea..
Thank you for any comment and sharing experience..