Could I analyze just a few genes of a BAM file?
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5 weeks ago
abdi.zhr26 • 0

Hi all, I want to analyze the DE of 14 genes in some patients. Can I download and analyze just the BAM file of 14 genes (plus housekeeping)? or I need the BAM file of whole genes for normalization?

RNA-Seq BAM • 300 views
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BAM files don't have genes, they have sequence reads and map locations. By the majority of methods it's the same amount of work to count reads on all genes as it is on your 14 genes + housekeeping. And you won't even know if your housekeeping genes really are doing what you think they are unless you see them amongst all the genes with which they are supposedly keeping house. In other words, you need all the data to make sense of it - even if you choose to focus on just your 14 genes, as others have said.

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5 weeks ago
ATpoint 49k

Comment: BAM file download for just a few genes

As said before you should not do that, explanation in the linked comment. Reads are not independent of each other, and most DE tools rely on a large number of genes with most not being DE to accurate normalize and estimate dispersion. Especially if you are new to this do not make custom pipelines, just download the whole thing and run it through an established pipeline, then later filter for the genes you want from the results table. There are often no reliable shortcuts in bioinformatics, especially not if you are not an expert in the process.

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