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Recent Replies
Comment: dedup STAR transcriptome file using umi_tools
by
i.sudbery
20k
You should definitely be able to use samtools ti sort and then index the transcriptome bam. We've done this many times.
Comment: dedup STAR transcriptome file using umi_tools
by
Ar
★
1.1k
Yes, you are right. I plan to do this. Thanks!
Comment: dedup STAR transcriptome file using umi_tools
by
rfran010
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1.3k
How about deduping based on the genomic bam, then filtering the transcriptome bam based on the reads leftover. Maybe some extra work, but m…
Comment: dedup STAR transcriptome file using umi_tools
by
Ar
★
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Yes, I am using the NEB's NEBNext UMI adaptors for the bulk RNA-seq samples.
Comment: dedup STAR transcriptome file using umi_tools
by
Ar
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Thanks for the reply. STAR generates two different bam files. One is the genome based and the other one is the transcriptome based. I am ab…
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Maybe consider seriation/ordination as an alternative.
Comment: dedup STAR transcriptome file using umi_tools
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i.sudbery
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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 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!
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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