Questions tagged [read-correction]
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7 questions
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Assessing Quality of Error Correction
The main idea:
Given fastq/fasta files containing reads(simulated from ref. genome, with errors introduced) and another file with the ground truth(simulated but without errors) and then the resulting ...
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If fastp output is not a good measure of FASTQ correctness, what is?
In the beginning of my pipeline, I just fed the paired reads (2 files) into fastp, with the default options, and assumed it would do a good job preparing the reads for the next step: alignment
But I ...
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Error when using awk command to trim sequence files
I am attempting to edit my fastq sequence files with an awk command from a published article. The sequence files are all ...
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Total read count of shotgun affected by few highly abundant sequences
I am building statistical models to analyse output from Illumina shotgun sequencing (HiSeq 4000) on stool samples (but RNA-seq data should behave similarily). The raw counts are a statistical sample ...
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At what stage of a transcriptome assembly is it better to perform read contaminant filter?
I'm trying to assemble a bivalve transcriptome. Since bivalves are filter feeders, their transcriptomes tend to be highly contaminated by bacteria, algae and whatnot. Since I pooled several ...
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How to force pilon to correct a reference with low coverage mapped reads?
I have mapped some reads to a reference and want to change SNPs in the reference to SNPs found in the reads, even at low coverage. For example, here is a screenshot of one reference in IGV that I ...
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Can I pilon-polish long reads with Illumina short reads to improve structural variant detection?
I have pacbio Sequel data at 50 x coverage for a strain of animal. I would like to find structural variants compared to the reference genome sequence. At the moment, I align my reads to the reference ...
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