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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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Sometimes I just want to trim "from xx bases onward" or "take just the first xx bases". In trimmomatic (considerably slower than atropos) this is obtained with the `HEADCROP` and `CROP` commands, resp…
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Hi There,
Thanks for samblaster, it's such a great tool. I wonder if you have considered supporting unique molecular identifiers at all? bcl2fastq supports adding them to the read name. So if a standa…
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On creating a record related to Museum für Naturkunde, Berlin, I was able to manually lookup and add a creator institution with automated link to their ROR records.
However, when creating the reco…
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### Enzyme, ADAR (proof-read and correct mistakes in RNA)
[**ADAR editing enzymes** are found in all multicellular animals and are conserved in sequence and protein organization. The number of ADAR g…
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Hi,
Biored ran efficiently, thank you for your help. I have one more favor to ask. How can I perform Named Entity Recognition (NER) and linking in the format required by BioRED for relation predict…
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Hi Salmon team
Are there plans afoot to support quantification of scRNA-seq data with unique molecular identifiers (UMIs)? UMIs are very commonly used in scRNA-seq data now, and correct quantificatio…
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**tl;dr**: 3-tag sequencing methods for bulk RNA samples contain known sample indices and UMIs and thus resembles sc-RNA-seq read formats. Do you have a recommendation on how to use Salmon and / or Al…
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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…
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This morning I am feeling very inspired by some work that @anastasiyaprymolenna , @sierra-moxon and others were doing last night. I'm talking about reviewing a [PR I made for simplifying ChemicalConve…