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Maybe consider seriation/ordination as an alternative.
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There are bulk protocols that include UMIs. Lexogen's CORRAL kits for example. Or NEB's NEBNext UMI adaptors.
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I am quite sure that you cannot use UMI_tools to deduplicate bulk RNA-seq. The different oligo adapter sequences on each bead introduce UMI…
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I don't know if any reason you shouldn't be able to index the bam produced by STAR, although you will need to sort them first.
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Hi ATpoint,
Thank you for your though provoking answer. Big fans!
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I'm wondering if this could work:
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You should contact the [GenePattern google group](https://groups.google.com/g/genepattern-help) - that's where you stand a higher chance of…
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What method are you using to identify markers and does it allow for nested designs?
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I will look into this. Thank you!
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example vcf:
```
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind1 ind2 ind3 ind4
chr1 100 . C …
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