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Recent Replies
Comment: Are there any preferred trajectory/pseudotime analyses that do not require an ar
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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.
Answer: dedup STAR transcriptome file using umi_tools
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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…
Answer: dedup STAR transcriptome file using umi_tools
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i.sudbery
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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.
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
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Hi ATpoint,
Thank you for your though provoking answer. Big fans!
Actually I have some normal cells in each sample, and I found good mixt…
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have you taken a look at csaw? https://bioconductor.org/books/release/csawBook/
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Have you tried running this in a fresh, clean `R` session with no other (unnecessary) packages and data being loaded into memory? How much …
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You most likely have duplicates somewhere in there in the column that is currently serving as index to (I am guessing) the counts DataFrmae…
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Expand your search by searching these (two) sequences against other sets of sequences.
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It's confounded. SCtransform is not doing anything in such situations and hatmony operates on a per-cell embeddings level and not per gene …
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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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vaellis
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I will look into this. Thank you!
Comment: count number of polymorphic sites among samples in vcf
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vaellis
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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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