Questions tagged [subset]

Subset is a defined section of the universal data set

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13
votes
4answers
668 views

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 ...
7
votes
1answer
403 views

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 ...
3
votes
1answer
860 views

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 ...
2
votes
0answers
50 views

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 ...
1
vote
1answer
44 views

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 ...
0
votes
1answer
28 views

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 ...
0
votes
2answers
3k views

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. ...
0
votes
0answers
184 views

Retrieving Co expression data from a Seurat object

I know that this topic has been discussed in other threads, but I never found a definitive answers (and maybe there isn't one) about assessing coexpression in single cell data. I want to assess the ...
0
votes
1answer
71 views

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 ...
-3
votes
1answer
55 views

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. ...