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Hi Alex,
I'm a bit confused about how deduplication works when you have multi-gene reads with same BC+UMI but a different set of mapped genes (e.g., due to sequencing errors). How do they get merge…
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When demultiplexed with a read structure indicating presence of UMIs (including `M`; ex. `146T8B9M8B146T` for a 9bp UMI), the resulting bam files include per-read UMI sequences via the [RX tag](https:…
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### Ask away!
To whom it may concern,
I am a user of wf-single-cell and I have some questions regarding the internal workings of the pipeline, specifically concerning the barcode and UMI correctio…
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Hi Alex,
Thank you so much for all of the resources you've provided to the community.
I'm working with PE150 bulk RNAseq data. My library adds an 8nt UMI to read2. I first extracted the UMIs fro…
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I used the trust-barcoderep-to-10X.pl to transform barcode_report, and got two questions:
1) Why are the numbers of umis and reads exactly the same in the results?
2) The raw_clonotype_id and raw_c…
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In some cases, we get FASTQs that have sample barcodes and UMIs in the read name and I we'd like to extract those. Is that possible?
See:
[1] https://help.basespace.illumina.com/files-used-by-bas…
nh13 updated
3 months ago
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Hello!
I would love your opinion or advice with our method, and I have a few questions about how UMItools extract with a regex works.
I have nanopore long reads with dual 18bp UMIs, one on eac…
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I have been using seqfold to design oligo constructs, but have run into issues when I use degenerate bases (like in unique molecular identifiers, UMIs). Would there be a straightforward way to allow f…
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Dear Daniel Lu,
Does maximum number of UMIs over all alignment positions mean: the maxium number of UMIs recovered at a given alignment position?
Done reading input file into memory!
Number of in…
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I like to use Github issues as TODO lists. First item of business: conflicting UMIs.
## The problem
UMIs are used by `demuxlet` and appear in the `UB` tags within the BAM file. When we create doub…