Questions tagged [subset]

Subset is a defined section of the universal data set

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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 ...
Lauren Sabo's user avatar
2 votes
3 answers

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: ...
Joy's user avatar
  • 21
0 votes
2 answers

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? <...
mmpp's user avatar
  • 371
0 votes
1 answer

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 ...
Hart Radev's user avatar
1 vote
1 answer

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 ...
GSQ's user avatar
  • 41
0 votes
2 answers

Subsetting from seurat object based on orig.ident?

I am pretty new to Seurat. I want to subset from my original seurat object (BC3) based on orig.ident. however, when i use subset(), it returns with Error. ...
Najeha Mohamed's user avatar
2 votes
0 answers

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 ...
Alex Cull's user avatar
1 vote
1 answer

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 ...
Itai Roth's user avatar
3 votes
1 answer

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 ...
ageans's user avatar
  • 131
-3 votes
1 answer

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. ...
user3698773's user avatar
7 votes
1 answer

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 ...
Scott Gigante's user avatar
13 votes
4 answers

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 ...
Konrad Rudolph's user avatar