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Recent Replies
Comment: What is the stance on optical duplicates in RNASeq?
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GenoMax
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> but optical ones are a technical artifact
Generally these are applicable only if your data was run on patterned flowcells (which may be …
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GenoMax
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> I have sequencing data from the NCBI SRAdatabase.
As in raw sequence data from dbGaP and not just counts? So you did get permission to …
Comment: MarkDuplicates RNASeq: A few samples look weird. What could be the cause?
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GenoMax
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Is this different data than what we were discussing in last two questions? Simple explanation may be that the quality of initial RNA was po…
Answer: MarkDuplicates RNASeq: A few samples look weird. What could be the cause?
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ATpoint
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What do you want to do? Differential analysis?
If so, ignore all these lowlevel metrics and see how samples compare in a PCA and how dow…
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Agreed, I also just tested it (with the following to try to mimic your setup exactly):
```bash
NXF_VER=24.10.5 nextflow run nf-core/genome…
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Hi Heureuse ... do you *have* to use a gVCF? Or could you use another format?
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The best choice would be use edgeR's built-in GSEA functionality provided by `camera` and `cameraPR`. These functions adjust for inter-gene…
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★
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Don't necessarily need to run `topTags`. Even with the `glmLRT` output, `lrt` say, the signed LRT statistic
```
z <- sign(lrt$table$logFC) …
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The coefficient (logFC) is the log2 expression change for each unit change in the continuous covariate.
The interpretation follows the usu…
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swbarnes2
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You can't show gene names, that's all. There's probably some setting like "show_row_names = FALSE". No one can help you without the code y…
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Thanks! I tried that. I’ve fixed the original "Invalid haplotype field" error by renaming all invalid haplotype fields, but now there’s a n…
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Have you tried turning it off and on again?
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Gene expression matrix are usually large, which causes overlapping gene names in heatmap and other plots. Following are few ways to improve…
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