Question: Are there any software packages available to calculate ploidy from RNA-Seq data?
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gravatar for JacobS
3.8 years ago by
JacobS890
Cleveland, Ohio
JacobS890 wrote:

I realize copy number variation from RNA-Seq data is a poor idea since expression differences between samples will confound copy number data, but what about general inferences of ploidy?

I have large RNA-Seq sets for >50 samples, and want to determine which are aneuploidy and which are not. Does anyone know of a means to do this?

cnv rna-seq ploidy • 1.5k views
ADD COMMENTlink modified 3.8 years ago by QVINTVS_FABIVS_MAXIMVS2.2k • written 3.8 years ago by JacobS890
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gravatar for QVINTVS_FABIVS_MAXIMVS
3.8 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.2k wrote:

Not sure, but if you have a bam file and samtools you can find the depth of coverage using the

$ samtools depth in.bam -r 1:100-200

It will print out a per-base pair depth of coverage, which can be normalized to the average coverage of the sample. So if the reads in the region have twice the coverage they are duplicated ( a normalized value of 1.5, as 0.5 is a heterozygous deletion)

You can perform the same task with

$ samtools view -c in.bam 1:100-200

and normalize by (read count / region size) * average read length / average coverage

Doing it systematically for RNA-seq I'm not sure, but you can probe around your bam files and see if there is an amplification.

ADD COMMENTlink written 3.8 years ago by QVINTVS_FABIVS_MAXIMVS2.2k

RNASeq has read coverage variation by gene usage, so every gene has a lot of difference between samples. Your coverage method won't work for ploidy. You must be thinking of genome sequencing.

I think we'd have to use SNP frequency and look for non-binary SNP sites.

 

ADD REPLYlink written 3.8 years ago by karl.stamm3.5k
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