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Hello,
I am interested to confirm an allele frequency for a SNV in BRAF gene using amplicon sequencing data. The length of amplicon is 271bp, and paired reads are 101X2. So there is a gap between t…
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Hello
Using graphmap 0.5.1 I want to overlap illumina MiSeq reads derived from enrichment sequencing. The reads are enriched for a large gene family. I would hope for large numbers of relatively shor…
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Is 'depthNorm = TRUE' in the scGAD function equivalent to BandNorm? Should I first use BandNorm and then calculate the scGAD for each gene and perform 'depthNorm = TRUE', or should I directly use 'dep…
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Hi,
I have a few questions about the software.
1. I attempt to use siRNA-seq to generate the DGE result. Will different sequencing methods affect the data interpretation and accuracy?
2. I am …
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Hi,
I am facing an issue with the burden test where the genotype goes to -nan or nan:
```
-reading in genotypes, computing gene-based tests and building masks...ERROR: Throw location unkno…
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May i ask 1 question:
if data is already pseudobulk object from scRNAseq data with logCPM value, how can i change it back to a seurat object with counts value? Can i still use above method to turn …
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May i ask 1 question:
if data is already pseudobulk object from scRNAseq data with logCPM value, how can i change it back to a seurat object with counts value? Can i still use above method to turn …
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May i ask 1 question:
if data is already pseudobulk object from scRNAseq data with logCPM value, how can i change it back to a seurat object with counts value? Can i still use above method to turn …
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Hi,
I ran inferCNV and got "infercnv.observations.txt" file. In the file, there are CNV values for just 1,089 genes. It seems that the genes that have zero CNV values across cells were filtered ou…
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Hi,
I'm curious if it is possible to use fastq files with reads from whole exome target-capture raw sequencing?
Thanks
Vinny