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Comment: bcftools error merging two VCFs: REF prefixes differ
by
iraun
6.1k
Then it looks like one VCF is based on GRCh37 coordinates and the other one on GRCh38. In order to merge, you need both VCFs to be based on…
Comment: bcftools error merging two VCFs: REF prefixes differ
by
Shane
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I don't think the liftover process was done for VCF_d but it does say reference=NCBI37. On the NCBI link here (https://www.ncbi.nlm.nih.gov…
Comment: bcftools error merging two VCFs: REF prefixes differ
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iraun
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I can't find information with respect to the reference genome used to call the variants in `VCF_d`, but in `VCF_p` it seems they used GRCh3…
Comment: Calculation of TMB on gene level
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smrutimayipanda
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I am asking about TMB calculation on gene level, especially TCGA data
Comment: Calculation of TMB on gene level
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smrutimayipanda
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can you please tell me why it is technically incorrect?
Answer: Gene enrichment analysis of prokaryotes gene
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dthorbur
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[Here](https://github.com/golden75/prokaryote_RNASeq) is a tutorial on how to use the R package DESeq2 for prokaryotic RNAseq analyses.
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Indeed, though it is a seek issue when accessing files **over HTTP and other network protocols**. So, unless there's something you didn't m…
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RM123
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Thank you for your help. I am comparing 4 groups, but as I have gene expression data I have a considerable number of boxplots to make. I fo…
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ATpoint
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And how should I know this? I cannot read minds, nor see your screen, data or anything. Please ask a good question with necessary details.
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edus_bioinfo
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Thanks. But they are already analyzed. Afaik it analyzes raw data. In my dataset for each gene there is score. I want to interpret the data…
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Hello again.
Yes, you can conduct GWAS using binary trait data, but it comes with a whole suite of complications. See [this](https://ww…
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RM123
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Hello Dariober,
That seems like a good solution, however I'm pretty new to R. Could you tell me how I can do that?
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Nicolas Rosewick
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Not really a bioinformatics related question. Start by looking at R tutorial, there is plenty of them online e.g. : https://www.statmethods…
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fracarb8
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You did not add the screenshot.
Answer: BED files
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Alex Reynolds
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Generically via `bedmap`:
```
bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed
```
The `annotations.bed` fil…
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