Questions tagged [subset]
Subset is a defined section of the universal data set
13 questions
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How to subset BAM file based on read length range (120-180) bp?
Hi I'm wondering how I can subset a BAM file based on read length. Precisely I want just read lengths of 120 to 180 bp reads in the new BAM file.
I'm trying several way, but none of them giving the ...
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I am trying to create a subset of 10k variants from 25-30 unmapped contigs of a g.vcf file including the header
My objective is to take a g.vcf.gz file and from 25-30 unmapped contigs with titles like "NW_020192317.1", I want to make a subset of ~10k variants from each of the unmapped contigs and make ...
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Seurat: Error in FetchData.Seurat(object = object, vars = unique(x = expr.char[vars.use]), : None of the requested variables were found:
I was trying to do subsetting via:
pbmc = subset(pbmc, subset = nFeature > 1000 & nCount > 4000)
R returns:
...
- 21
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subsetting more than one ccle sample
I'm working with the CCLE dataset and I'm trying to subset the data to just 3 cell lines of interest but not sure how to it.
Currently, I have been subsetting one by one but is there an easier way?
<...
- 391
0
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1
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83
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Differential expression analysis for a subset of transcripts
I want to check the differential expression of a specific class of transcripts (say, long non-coding RNAs) using DESeq2. Now, I know that the normalization step takes into account the total number of ...
- 113
1
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1
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83
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Metagenome simulation from a concatenated FASTA file
I am trying to simulate metagenome sequencing. So I will start with a file with a lot of concatenated genomes. From there, I would like to randomly extract 10,000 sequences of length 200bps.
I got ...
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Subsetting from seurat object based on orig.ident?
I am pretty new to Seurat. I want to subset from my original seurat object (BC3) meta.data based on orig.ident. however, when i use subset(), it returns with Error.
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2
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383
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Subsetting SNPs with specific exclusion criteria using bcftools
I am trying to subset SNPs from 32 cultivars. I have the following exclusion criteria:
>20% missing data
SNPs present in less than 50% of genotypes
Each genotype must have at least 50% of included ...
- 21
1
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1
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55
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choosing a good representative genome subset
I'm trying to build a genomic database for DNA alignments.
I started with NCBI accessions, but the data is very multiplicative, so I want to use subset of [max] N different strains for each specie.
my ...
- 35
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1
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Subsetting of object existing of two samples
I have a Seurat object existing of an aggregate of two samples namely; RD1 and RD2. I am trying to make a subset of each sample. But it's not really working. I manage to make a subset of the cells but ...
- 131
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simple data subsetting on r
I have a big df like following (pseudo) df and I want to retrieve values in different col. according to the rows in the first col.
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- 199
7
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Split FASTQ and matching BAM into matching chunks
I am running a slow downstream analysis on a large set of nanopore reads (approx 3 million), and would like to split them into smaller chunks, run the analysis in massively parallel, and then ...
- 2,173
13
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4
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How do I efficiently subset a very large line-based file?
This has come up repeatedly recently: I have a very large text file (in the order of several GiB) and I need to perform line-based subsetting for around 10,000 lines. There exist solutions for ...
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