Normalize BAM file
I need to normalize the BAM file. The variance file I'm having based on BAM file does not represent the normalized reads. If I use bamCoverage or bamCompare, I can't have data in the tabular format.
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arif.ashraf.opu •
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Please tell us what you mean by "normalize". I have personally never heard of normalizing BAM data.
Actually, I'm using RNA-seq data to find SNPs in the mapping population. When I calculate the SNPs based on the BAM file, these variations do not mean the real variation between wild-type and mutant. So, I was trying to normalize the reads or SNP counts should come from normalized reads. Does it make sense?
You're calling variants from RNAseq data, correct? What protocol are you following and what do you think is causing these unreliable calls? Could it be that you're using a protocol meant for DNA Seq data on RNA Seq?
Well. If you have to call variant based on RNA-seq data, what will be your approach?
Tell me what you have tried and where you're facing a problem, and I will try my best to help you. Right now, you're asking me to do your job for you, which I will not do.