Fpkm Or Rpkm Equivalent For Exome Sequencing Data

Question

[pm2013]

Hi

I am fairly new to exome sequencing and not familiar with tools available for analysis of this kind of data. I need to calculate from an exome sequencing dataset that I aligned using BWA, the equivalent of FPKM/RPKM for RNAseq data. I was wondering if there was any kind of tool that I could use directly (e.g cufflinks for RNA-seq) that would give me this info.

Any help is appreciated.

Thanks

[venks]

Please be specific.. what are you trying to find? call variants?

[pm2013]

Hi I am not looking to call variants. I already know how to do that..but am just looking for coverage(?) of specific genes...just like you get FPKM for genes in RNA-seq.

[pm2013]

Thank you all. I will try out your suggestions. They were very helpful.

[Obi Griffith]

You are welcome. For next time, probably better to add your thank you as a comment on one of the answers or as a comment to your original question, rather than as an "answer" to your question.

Answer 1

[Obi Griffith]

It doesn't sound like you want FPKM/RPKM exactly. Those metrics normalize for gene length and also library depth so that (in theory) you can compare transcript expression levels between genes and libraries. This doesn't make sense if you want to understand how well your exome-seq experiment has worked. If one library has twice as many reads and gives you twice as good coverage you want to know that, not try to normalize that difference away, correct? You probably want average depth of coverage for a particular exon/gene or averaged across exons/genes. Search the forum for "exon coverage calculation" and you will find many posts on this topic.

• Calculate per exon/per gene coverage
• calculate exon coverage using SAMtools
• tools to calculate average coverage for a bam file?
• Calculate coverage from BAM file
• How to calculate the coverage of a specific interval based on data from a bam file
• NGS and coverage of exons

Answer 2

[venks]

Try using qualimap it should give you coverage information.

Answer 3

[Alex Paciorkowski]

You don't mean FPKM or RPKM. You want to use GATK's depthofcoverage walker. You can give it as inputs your bam files and your target, and get depth of coverage across your entire target, or if you just want depth of coverage of a certain gene or genes you can use the -L option to input a file with those specific genes. Take a look at GATK's documentation for the correct formats of the target input files.