Questions tagged [umi]
The umi tag has no usage guidance.
5
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1answer
102 views
Moving UMI from tag into read name
I have a bam file with Unique Molecular Identifiers (UMIs) for each read present on the RX tag ( such as RX:Z:TGAGAAGGG), as expected by picard and fgbio tools.
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1answer
215 views
Add tags to the read pairs in a bam file
I have a bam file from paired-end sequencing, in which each R1 has the RX tag assigned (via UMItools group) denoting a Unique ...
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2answers
188 views
How are UMIs used to dedupulicate in Drop-seq tools?
The module DigitalExpression which is part of the popular Drop-seq tools digitally count gene transcripts.
The manual is not very clear on how exactly it resolves ...
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2answers
2k views
BAM to gene expression matrix (UMI counts per gene per cell),10X
I am trying to reproduce some results of a scRNASeq experiment. However I am new to the server-side aspect of such analyses and am very confused at the moment.
The data provided by the authors of the ...
1
vote
1answer
60 views
Article GEO gives counts that are not integers. Should UMI counts be integers?
I thought that UMI counts are always integers, but when I opened several datasets provided by GEO I got confused because in some ...
