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Recent Replies
Comment: Example of ClinVar pathogenic variant where the reference allele is pathogenic?
by
GenoMax
152k
It is likely this one --> https://www.ncbi.nlm.nih.gov/clinvar/variation/36924/
From original search here --> https://www.ncbi.nlm.nih.gov…
Comment: Example of ClinVar pathogenic variant where the reference allele is pathogenic?
by
a615ebfb
▴
50
Thanks, Jeremy!
Not sure if I retrieved the right one but it does not show up as pathogenic on the website: https://www.ncbi.nlm.nih.gov/…
Answer: Example of ClinVar pathogenic variant where the reference allele is pathogenic?
by
Jeremy Leipzig
23k
For REF/REF entries the ALT is '.'
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
gunzip -c "c…
Answer: Functional Analysis Using EMU Output – Has Anyone Tried This?
by
andres.firrincieli
3.9k
You can't use EMU with tools like PICRUSt2 because it doesn't produce typical outputs such as OTUs or ASVs. EMU works more like a read-lev…
Comment: featureCounts -t option not working in v2.0.8?
by
rfran010
★
1.5k
Try the older version? Is it the same GTF from before?
I would guess a formatting issue with the 9th column, but I haven't tried this ver…
Comment: should I remove the transcripts from annotate peak region in ATAC-seq
by
rfran010
★
1.5k
It's not clear to me what you mean. How could you tell it's annotated to the transcript and not the genic region in the genome?
Generally,…
Comment: mm10 blacklist regions detailed information
by
GenoMax
152k
If you are OK with ENCODE blacklists then you can find a BED file with the information at: https://github.com/Boyle-Lab/Blacklist/tree/mast…
Comment: identify unmapped regions
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GenoMax
152k
> We've created a coverage file of the aligments against the GRCh38 reference genome
Are you referring to regions that are hard to align r…
Comment: filters used in mutation discovery from RNAseq data
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GenoMax
152k
One line questions are never a good way to describe what you are trying to do and without that information you are not likely to get any us…
Answer: martCheck - Error - You must provide a valid Mart object - for running HoneyBADG
by
mete.han.celebi
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Hello everyone,
I have fixed the issue.
Here how I fixed:
mart.obj <- useMart(
biomart = "ENSEMBL_MART_ENSEMBL",
da…
Answer: How to Specify Power Parameter for Adjacency in modulePreservation() (WGCNA)
by
andres.firrincieli
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multiData can contain your adjacency matrices. Then in `modulePreservation()` set `dataIsExpr = FALSE`
Comment: Should matched samples (not paired) be included in the DESeq2 design model?
by
i.sudbery
21k
No thats not what I mean.
When you run DESeq, if fits values to each of the coeffients that you specify. You then compute p-values on som…
Comment: Single-cell RNA Sequencing - transcript abundance estimation using Alevin-Fry
by
wooh
•
0
Thank you that makes sense. When previously doing this it seemed the quantification result had assigned exact equal values of two transcrip…
Comment: Trajectory Analysis scRNA-seq with one cell type and two developmental stages
by
npont
▴
10
Yes I would agree for clustering, but the way I define my cell type is not based on clustering:
I define cells as being of my type of inter…
Comment: Should matched samples (not paired) be included in the DESeq2 design model?
by
marieke
•
0
Ah yes, looking at the PCA makes sense, thanks!
I'm not sure I understand your last paragraph, though. With 'running tests', do you mean r…
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