Tag: Quantseq

Quantseq 3′ seq alignment with kallisto

Quantseq 3′ seq alignment with kallisto 0 Hi All, In my current work, I am using Kallisto in 3 prime RNA seq data (read length 55bp) from melanoma samples. I am ideally expecting quantification mapped to only one transcript of my gene (canonical) as Quantseq 3′ seq quantifies one read…

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How many runs can be performed with the QuantSeq kit?

The QuantSeq 3′ mRNA-Seq kits contain enough components to generate up to 96 reactions for manual or automated library preparation. Therefore, the provided reagent volumes should be sufficient to run all reactions at once on your liquid handler. However, if you want to split your kit into several machine runs…

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QuantSeq 3’ mRNA-Seq Library prep kits: Lexogen

QuantSeq 3’ mRNA-Seq Library Prep kits from Lexogen offers cost-efficient analysis of differential gene expression via 3’ mRNA-seq library preparation. Requiring fewer reads per samples and capable of multiplexing a high number of samples on a single sequencing lane, the 3’ mRNA-Seq technology simplifies your gene expression projects with no…

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RNA-Seq Data Analysis Software – Isogen Lifescience

BlueBee Genomics The BlueBee platform is a production-ready, robust infrastructure that is easy to use for any researcher. It can be used for analysing data from QuantSeq, CORALL, and SLAMseq experiments. There is no prior bioinformatic experience required. Each purchased QuantSeq and CORALL kit includes a code for free data…

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Exclude pseudogenes and lncRNA’s from DE-analysis?

Hi all, Let’s start off to thank the ones that helped me lately. I almost feel bad for how many questions I have asked in the last weeks, but the answers were always of great help, so thanks for that! And yet I have another question. As described in my…

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RQN value for Quantseq experiment

RQN value for Quantseq experiment 0 Hi guys, I read some conflicting results about the minimum RQN value in Quantseq experiments. What minimal RQN value is acceptable for a human Quantseq experiment? Moreover, is it possible if the majority of the samples have a RQN value > 7, and some…

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Correcting for leukocyt count in QuantSeq analysis

Correcting for leukocyt count in QuantSeq analysis 0 I am conducting a human white blood cell (WBC) QuantSeq analysis. I have heard some stories about the need to correct for WBC count as this could influence the results. I haven’t been able to find literature about this, so my question…

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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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MD plot for every sample (?!)

MD plot for every sample (?!) 0 Dear all, I am conducting a QuantSeq analysis and in the manuals I find online one of the steps include making an MD-plot for every sample. This is considered data exploration as well as a quality control check, this of course sounds very…

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My bioinformatics story

My bioinformatics story 1 Hi all! I am new to the bioinformatics world and due to circumstances I have been given the complete responsibility to perform a human transciptomics data-analysis without bioinformatic background and for now also without supervision. This whole project feels like a big challenge, finding a puzzle…

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Filtering lowly expressed genes

Hello all, I have a quick RNAseq (Quantseq) question for you all! I am analyzing the Quantseq data for 500 patients and am finding my way through the bioinformatic forest. Currently I am working on a way to filter out lowly expressed genes, and I am using the Bioconductor package…

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