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Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
The Biostar Herald for Monday, May 20, 2024
Answer: plink2 cannot make bed file
Answer: plink2 cannot make bed file
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Recent Replies
Comment: How to calculate cell type frequency between two groups in single cell data
by
Sara
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Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
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Deepthi
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I unzipped the fastq files to check whether reads are trimmed adapter or not. I have checked the quality control using fastqc they are go…
Comment: Mutation counts corrected by number of samples
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Ram
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> I want to compare the number of mutations This comparison will give you literally no useful information.
Answer: How to scrape BioMart data from https://sorfs.ugent.be/ website
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Pierre Lindenbaum
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something like: seq 1 100 4377380 | while read F ; do wget --no-check-certificate -O - "https://sorfs.ugent.be/database/micrope…
Answer: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
The variability explained by the variables provided to `group.by.vars` is what Harmony will try to remove. Assuming you want to remove the …
Answer: Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
by
Jeremy Leipzig
22k
That SNP is in an HLA gene which has had a lot of attention and improvement over the years, ranging from kits to software to the reference …
Comment: Overlapping clusters for different biological conditions: Seurat, UMAP
by
Bastien Hervé
5.3k
What is the need of PBMC in your analysis ? If none, removing them from the beginning will allow your clusters to be more specific to your …
Answer: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
I believe `sample_id` are your replicates in either `patient` or `control`. You can do it manually by normalizing the number of cells yo…
Answer: bfctools merge [E::hts_open_format] Failed to open file
by
j.f.akers
• 0
I think the program is trying to open a .vcf.gz.csi file rather than the actual data which is the .vcf.gz file, the csi file is not data, j…
Comment: LDhat lookup table
by
NÚRIA
• 0
Hi! Did you manage to fix this? I run convert successfully on 60 unphased diploid samples (1500bp), hence I used lktable available in LDh…
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI
by
F110152169
• 0
It's Parkinson's disease. How do I get the right order?
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
QX
• 0
yes but they did not reply
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
fracarb8
★ 1.7k
Looking at both `nCount` and `MT` the profile are cut at your thresholds, suggesting that you simply don't have cells with >2000(ish) genes…
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
Pierre Lindenbaum
162k
did you ask the authors to restore their server ?
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
sc_analysis
• 0
Yes. But after applying: merged_seurat_objects_filtered <- subset(x = merged_seurat_objects, subset = nFeature_RNA > 200 & nFeature_R…
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