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Answer: plink2 cannot make bed file
Answer: plink2 cannot make bed file
Answer: Conda, bioconda, anaconda, are they different?
Answer: Conda, bioconda, anaconda, are they different?
Gene Set Enrichment Analysis
Comment: Unexpected read length from NGS
Answer: Unexpected read length from NGS
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Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
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Pierre Lindenbaum
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did you ask the authors to restore their server ?
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
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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…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
fracarb8
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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
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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
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ATpoint
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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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Deepthi
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Thanks will check and update here.
Answer: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
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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…
Comment: Annotating single cell data automatically
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Francesco
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- 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
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You are not subsetting based on `nFeature`. You are subsetting based on `nFeature` **AND** `nCount` **AND** `perc mt`.
Answer: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
txema.heredia
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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] …
Comment: Unexpected read length from NGS
by
QX
• 0
thank you all!
Comment: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool
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Initially, I tried using Samtools and BCFtools, followed by running a script in Python (PyCharm) to measure nucleotide diversity![nucleoti…
Comment: Best Practice On Variant Discovery For Bacteria?
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Ruqaiya
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I used HaploTypecaller but my plasmid reads are not present in the output vcf file ... but it's there in my input file
Answer: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool
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Variants should be called using a specialized mitochondrial variant caller, e.g.: [GATK Mutect2 CallMt][1] Then, pi, Tajima's D, and oth…
Comment: Splitting query fasta file for Diamond Blastp make the process faster?
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kmat
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I used `seqkit split` to divide the query FASTA file into 10 parts and then ran `diamond blastp` on each file using 44 threads. The process…
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