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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 LDhat…
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
★
1.6k
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
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…
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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