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Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI
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
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
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j.f.akers
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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
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NÚRIA
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Hi! Did you manage to fix this? I run convert successfully on 60 unphased diploid samples (1500bp), hence I used lktable available in LDhat…
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI
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F110152169
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It's Parkinson's disease. How do I get the right order?
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
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QX
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yes but they did not reply
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
fracarb8
★ 1.6k
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
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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…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
fracarb8
★ 1.6k
This [paper][1] provides a comparison of the three methods in different settings. [1]: https://genomebiology.biomedcentral.com/articles…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
Deepthi
• 0
pop up with sam error . Error reading _rstarts[] array: 21720, 23124
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
ATpoint
82k
See me edit I just made for the fastq check.
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
Deepthi
• 0
Thanks will check and update here.
Answer: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
ATpoint
82k
bowtie -x idx file.fastq | samtools view -o out.bam You might be messing up things with these positional arguments. Use this above. Us…
Answer: Annotating single cell data automatically
by
Francesco
▴ 10
- In order to run Azimuth: ``` AzimuthClusters <- RunAzimuth(seurat_obj, reference = "pbmcref") ``` - singleR ``` surveyRefere…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
fracarb8
★ 1.6k
You are not subsetting based on `nFeature`. You are subsetting based on `nFeature` **AND** `nCount` **AND** `perc mt`.
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