Questions tagged [umi]
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7 questions
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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 ...
- 189
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3
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104
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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 ...
- 21
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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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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 ...
- 121
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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 ...
- 600
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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 ...
- 910
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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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