Questions tagged [umi]

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Single Cell RNASeq Knee Plot - Collapsed vs Non-collapsed Reads

I am trying to adapt combinatorial index reads with some modifications for long read sequencing; it's a custom approach, not a commercial kit. I have a question about using Knee Plot for identifying ...
user3377241's user avatar
2 votes
3 answers
96 views

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 ...
Wei Feng's user avatar
0 votes
1 answer
524 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. ...
SPPearce's user avatar
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1 vote
1 answer
857 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 ...
SPPearce's user avatar
  • 121
1 vote
2 answers
280 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 ...
Sebastian Müller's user avatar
5 votes
2 answers
3k 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 ...
h3ab74's user avatar
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2 votes
1 answer
186 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 ...
Nikita Vlasenko's user avatar