Questions tagged [data-preprocessing]

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How to access BOLD timeseries data using atlas-Schaefer2018_desc-400Parcels with Python?

So basically I have this code ...
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2 answers
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Replacing column 1 in file1 with matching ID's in file 2

I have downloaded two files: File1.csv from: https://depmap.org/portal/download/data_slicer/download?file_path=20220227%2F3c335b7d-c18e-4788-b2e6-512d71f0a339%2Fexport.csv&name=Metabolomics.csv ...
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Reading in external single cell data

I'm trying to read in an external single cell dataset from https://www.nature.com/articles/s41467-020-16164-1, but I am having trouble reading in the count matrix. counts found here: https://www.ncbi....
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replacing periods with hyphen

I am a software engineer and not a bioinformatician. I am looking at some code where they are looking at aligned proteins that are in the A2M alignment format (https://compbio.soe.ucsc.edu/a2m-desc....
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Dictionary and index of vcf for base recalibration step

I need suggestions in creating index and dictionary with vcf files. For the base recalibration step, I downloaded Homo_sapiens_assembly38.known_indels.vcf.gz from the given link: https://console.cloud....
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Mapping ICD9 codes in UKBB data to PheCodes using PheWAS package

I am working on the UKBB data and trying to specify cases and controls by converting ICD9 codes to PheCodes. I have input data (icdt) where the first column (f.eid) is patient IDs and the remaining ...
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How to Read SCF file in Python?

Is there any way that I can read SCF file in python like in R using sangerseqR, I have tried with Biopython, it seems it does not support this format.
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Filter rows of VCF file for Match=EXACT?

How do I remove rows in a VCF file on 1kGenome column, where Match=EXACT using bash ?
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How to extract column from a matrix matching the another file (sample file)

I have two files master file.txt and sample.txt master.txt ...
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Print specific columns in a matrix on the basis of sample id's in the header

I have a matrix file (expression.txt) in which the first column is a gene_id and from the second column the sample id's start. This matrix has 20,000 columns with sample id's corresponding to ...
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TCGA dataset: different accession IDs mapped to same location?

I'm currently working on TCGA miRNA dataset. After constructing a reads matrix, I'm trying to find the isoform sequence. In my data, I have the genomic location (isoform_coords). I found that entries ...
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how to train a gene dataset with a nearest shrunken centroid classifier?

I have a data file named "geneexp.csv". the data contains information about gene expression of three different cell types (CD4 and CD8, CD19) I want to classify cells by performing the ...
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Extracting concatenated metadata from a column in R

I've downloaded some ChIP-seq data from www.chip-atlas.org and I want to use this to conduct some enrichment tests with genomic regions from my experiment. The .bed file generated by that website is ...
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2 answers
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How to get the genomic sequences from a blat result?

Assume we have a query.fa file that contains sequences and we run: ...
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How to aggregate multiple MAF files together?

I have cancer genomic data (tumor/normal whole exome sequencing) from 50 patients that received the same type of treatment, half of whom responded. These come in the form of 50 .maf files, along with ...
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Is there a command line tool to split a SAM/BAM file by CB (cell barcode) tag?

I have a BAM file from a single cell sequencing experiment. Each read has had the cell barcode annotated in the CB tag. Some reads do not have a ...
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How to run trimmomatic in HPC

Sorry if this has been asked before, I've done a quick search and I don't think there's an easy explanation for me to understand. I'm really new to bioinformatics/RNASEQ analysis, having only taken ...
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3 answers
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Edit all the fasta headers using awk

kindly your comment highly appreciated have more than 4k header sequences look like: ...
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2 answers
37 views

Appropriate value to replace outliers in clinical studies

I am working on clinical study where I am focusing on binary classification problem. There are few variables which has outliers. I am trying to know which would be the right value to replace ...
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Blood analysis devices: how and where is the data saved

I've read that there are blood analysis devices that can automatically determine the data for each specified analyse. You can expect to get the results in less than a day. Q: How and where do they ...
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1 answer
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How to remove degenerate sequence (N4) at the 5' and 3' of the reads?

I have to analyse GSE114327. For that, I use GSE instruction based on GSM3139597. In that data processing section has written: FASTQ reads were subjected to adapter removal (cutadapt) per ...
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What are the right parameters to trim a small RNA transcriptome with trimmomatic?

I'm having some problems with finding the right parameters to trim my small RNA Illumina reads (51 nt long) with Trimmomatic. Before trimming, one of the samples (21M reads) looks like this: So for ...
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3 votes
1 answer
250 views

Fast processing of fastq data

I am trying to write python script for customized filtering for fastq file (size >3 GB). My proposed script is as follows: ...
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4 votes
2 answers
2k views

"Sequence Duplication Levels" module still fails after pre-processing Illumina data

I want to ask about why the sequence duplication levels are high after I trimmed by using Trimmomatic? I am using the following Trimmomatic operations: ...
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2 votes
4 answers
306 views

Is there a read mapper that allows input in SAM format instead of FASTA/FASTQ?

When we get raw sequenced reads in FASTQ format, we usually need to do some pre-processing (QC, demultiplexing, etc.) prior to sequence alignment. The only way to register the results of this ...
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1 vote
0 answers
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case/control phenotype prediction - population stratification with R

I'm struggling these last days on a case/control phenotype prediction problem based on genotype (individual x SNPs with more than 10k individuals and approx 18k SNPs encoded as 0,1,2). Thanks to PCA ...
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1 answer
345 views

What is a standard approach to binarize microarray gene expression data?

I am using gene expression data from a microarray dataset for the purpose of learning the network structure of genes in the dataset. Now to do this I need to binarize my data, i.e convert the data ...
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1 answer
113 views

How hard is it to clean and QC gene expression microarray data?

I am a PhD student working on developing ideas for my dissertation papers. One of my planned papers will be working with some (human) gene expression data. I have had a class on working with gene ...
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4 votes
1 answer
990 views

Inspection of gene expression in scRNA-seq data

I am running the data preprocessing pipeline for scRNA-seq data presented here. 3.8.6.1 Gene expression In addition to removing cells with poor quality, it is usually a good idea to exclude genes ...
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6 votes
1 answer
218 views

Scaling by linear regression against the number of reads

I am trying to build the preprocessing pipeline presented in The Tabula Muris Consortium et al. (pp). It is a pipeline to preprocess single-cell sequencing data. There is one step that is not clear: ...
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