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Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
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did you ask the authors to restore their server ?
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sc_analysis
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Yes.
But after applying:
merged_seurat_objects_filtered <- subset(x = merged_seurat_objects, subset = nFeature_RNA > 200 & nFeature_R…
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This [paper][1] provides a comparison of the three methods in different settings.
[1]: https://genomebiology.biomedcentral.com/articles…
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pop up with sam error . Error reading _rstarts[] array: 21720, 23124
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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
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Thanks will check and update here.
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bowtie -x idx file.fastq | samtools view -o out.bam
You might be messing up things with these positional arguments. Use this above. Us…
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- In order to run Azimuth:
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surveyRefere…
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fracarb8
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You are not subsetting based on `nFeature`. You are subsetting based on `nFeature` **AND** `nCount` **AND** `perc mt`.
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Update:
I ran CellBender on these samples and compared its results with SoupX and DecontX.
vs SoupX:
![cellbender vs SoupX][1]
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Variants should be called using a specialized mitochondrial variant caller, e.g.: [GATK Mutect2 CallMt][1]
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