User: i.sudbery
i.sudbery • 2.1k
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Posts by i.sudbery
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Comment:
C: TCGA FPKM-UQ method theory
... You can only include batch in your design model if you are going to do differential expression. ...
written 9 days ago by
i.sudbery • 2.1k
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Comment:
C: TCGA FPKM-UQ method theory
... The rlog function from DESeq will allow correction for batch effects I think, this takes read counts. And limma has a "removeBatchEffects" function, it would take your FPKM_UQ numbers, although its not ideal. . ...
written 9 days ago by
i.sudbery • 2.1k
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1
answer
177
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Comment:
C: TCGA FPKM-UQ method theory
... Depends on what you want to use it for. If your main object of study is looking at how each gene varies between between samples, then I would use either DESeq or EdgeR normalised read counts. I'm pretty sure that read counts for TCGA are available somewhere. You would then model expression levels as ...
written 10 days ago by
i.sudbery • 2.1k
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99
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Comment:
C: Identifying UMIs from fastq files
... Yes, from there:
> Next-generation sequencing on Illumina NGS systems miRNA sequencing
> libraries prepared with the QIAseq miRNA Library Kit can be sequenced
> using an Illumina NGS system (MiSeq® Personal Sequencer, NextSeq 500,
> HiSeq® 1000, HiSeq 1500, HiSeq 2000, HiSeq 2500 and GA ...
written 12 days ago by
i.sudbery • 2.1k
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99
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Comment:
C: Identifying UMIs from fastq files
... But the manual says to only do single end sequencing ...
written 12 days ago by
i.sudbery • 2.1k
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99
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Comment:
C: Identifying UMIs from fastq files
... Yeah, but which end is the sequencing adaptor on? And how many bases is the UMI. ...
written 12 days ago by
i.sudbery • 2.1k
2
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177
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Answer:
A: TCGA FPKM-UQ method theory
... The reason for the upper quartile normalisation is because of proportionality and sequencing real estate issues.
Consider two samples with the following number of transcripts per gene:
| A | B |
gene 1 | 10 | 10 |
gene 2 | 10 | 10 |
gene 3 | 10 | 10 |
...
written 12 days ago by
i.sudbery • 2.1k
0
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99
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0
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Comment:
C: Identifying UMIs from fastq files
... UMI-Tools will extract the UMIs from reads, and then once the reads are mapped can be used to deduplicte based on the UMIs in an error correcting manner. But what I can't find from the QIAgen material is how long the UMI is and which end of the read it is on. ...
written 12 days ago by
i.sudbery • 2.1k
0
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99
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Comment:
C: Identifying UMIs from fastq files
... Do you know the library prep with which the sequencing was performed? ...
written 13 days ago by
i.sudbery • 2.1k
0
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99
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Comment:
C: Identifying UMIs from fastq files
... Generally speaking Unique Molecular Identifiers (UMIs), Unique Molecular Indexes (UMIs) and Random Molecular Tags (RMTs) reffer to the same thing. Although, as they are not well defined terms it is possible you will find someone using them for different purposes. ...
written 13 days ago by
i.sudbery • 2.1k
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For UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
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