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@atpoint the question is updated. the first command shows how the index is built.
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You can have a look on my answer. I have post it below.
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Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2).
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Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
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It did not help either. But I got the answer [here][1]
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https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
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