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Questions tagged [data-preprocessing]

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18 views

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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Is there any method for an automatic linking of metabolite names to their database identifiers (eg. HMDB)?

I collated a list of metabolites across different studies (>3000 entries) with: overlapping and synonymic names amino acids, organic acids, lipid targets [TAG, DAG, phospholipids], carbohydrates. ...
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63 views

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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96 views

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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144 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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249 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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3answers
160 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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45 views

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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1answer
172 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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1answer
68 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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430 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 ...
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171 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: ...