Questions tagged [umi]

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Can we do NGS library preparation using UMI with large amount of DNA input?

We know that in next-generation sequencing (NGS), the unique molecular identifier (UMI) can reduce or eliminate sequencing or PCR errors and result in very high accurate data. Therefore, UMI is widely ...
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0 votes
1 answer
224 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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  • 121
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1 answer
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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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  • 121
1 vote
2 answers
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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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5 votes
2 answers
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 ...
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  • 796
1 vote
1 answer
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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 ...
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