Tag: Spike-Ins

normalization of ChIP-seq data by using the spike-ins or by using total library sizes

Dear all, This question may have been asked before, I have searched the mailing list and I can not find an answer. The question is about the correct way of setting the SizeFactors() in DESeq2 in 3 situations. I would like to double check with you. Although the R code…

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TAmiRNA NextGen Sequencing pipeline

Diagnostic innovator TAmiRNA now has in its product pipeline an innovative NGS technology for absolute quantitation of miRNAs and other small RNAs , the miND® (microRNA Next-Generation Sequencing Discovery) spike-in. The miND® spike-in has been developed for small RNA sequencing experiments and absolute quantitation of microRNAs in any biological matrix…

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what can cause high(> 80%) spike-ins and low read count (

what can cause high(> 80%) spike-ins and low read count (<100 reads) in low complexity ampseq run 1 Hello, I have data output from low complexity ampseq run. The read counts are very low (<100 reads per well) and the spike-ins% is very high (>80%) across all of the samples….

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Extracellular circulating miRNAs as stress-related signature to search and rescue dogs

Study approval was provided by the Research Ethics Committee of the University of Perugia (report n.2018-21 of 11/12/2018) according to Italian Ministry of Health legislation18. All methods were carried out following relevant guidelines and regulations and the study was carried out in compliance with the ARRIVE guidelines. Informed consent is…

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eli5 RNA Spike-ins : explainlikeimfive

I’m a data scientist trying to branch out into more bioinformatics/genetics. My tutorial is counting spike-ins, but his explanation was over my head: 1 – AnnData and Preprocessing spike-ins | Kaggle ” Because this is smartseq2 data, we may have spike-ins. An RNA spike-in is an RNA transcript of known…

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Use Spike-Ins or TMM-normalization

Use Spike-Ins or TMM-normalization 1 Hi all, Sorry for all my questions lately, but as a novice which has to figure out how to analyse QuantSeq data, this forum has been a great and indispensible help for me. I’m doing a human transcriptomics analysis where we have QuantSeq data for…

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