Questions tagged [illumina]
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71
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Why do people quality-trim paired-end reads?
To my understanding, as long as you have overlapping paired-end reads, most modern aligners/merge algorithms can handle the alignment of each read pair well, and don't benefit from less data (i.e. ...
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2
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short Read/percentage threshold for bacterium presence in metagenome
I have ~100 paired end short read human gut metagenome samples that I classified using Kraken2. Now I want to know if a specific bacterium is in any of those samples. As far as I've searched people ...
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Where to obtain fastq_illumina_filter
I'm setting up a snakemake pipeline for my lab, and I'd like to install fastq_illumina_filter. All links I can find point to this address for info on it, but the website seems to be down.
Is there ...
- 412
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15
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Binning then assembling sequencing reads
I am attempting to do something similar to the "Phylomapping" pipeline described in this paper: https://www.nature.com/articles/s41559-019-0914-2. I have sets of Illumina PE reads, that I ...
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cellranger-arc throws an error when demultiplexing
I have a multiome dataset from a 10x run I'm trying to demultiplex using cellranger-arc mkfastq.
The demultiplexing uses the ...
- 223
5
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83
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Can index hopping lead to more reads in samples?
We run multiple samples for sequencing on an Illumina NovaSeq machine. After converting the files to fastq format using bcl2fastq, we can see that we have some ...
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40
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Hybrid assembly versus polishing for hifi and illumina reads
I will have to carry out a project of assembly using hifi reads for which I have already illumina reads and I am wondering which of the hybrid assembly or polishing would be the best option for this ...
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2
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88
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How do I quantify a specific somatic variant?
I'm working with targeted Illumina sequencing data generated with DNA from diseased and healthy tissue (this is an age-related disease and is not cancer/neoplastic). My hypothesis is that the diseased ...
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Aside from the header info, is there any way to distinguish between sequences generated by MiSeq and MiniSeq platforms?
I am comparing Illumina MiSeq (using MiSeq v3 kit) and MiniSeq (MiniSeq High Output kit) instruments for sequencing E.coli and Salmonella. I am curious if there is any way to bioinformatically ...
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32
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Illumina Final Report seemingly giving impossible genotypes; how do I make sense of this file? [closed]
I am working with an Illumina-generated final report file from human genotyping; the MEGA chip I believe. It's in a massive .csv file I've been 'exploring' via unix commands on a compute cluster, ...
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28
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Does using a microarray chip that matches the chip used in training lead to higher explained variance of a polygenic score?
I'm trying to replicate an existing polygenic score (i.e. test the accuracy in a new sample), and want to know if matching the original study's microarray chip will improve the accuracy (that is, ...
- 598
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41
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Does pooled sample genotyping microarray analysis exist?
I want to genotype samples in small batches with a common microarray (e.g., the GSA). However, the cost is very high for small batches.
With a higher sample throughput/volume, per sample cost becomes ...
- 598
3
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1
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99
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How to interpret a GenomeScope plot?
I am working on a new sponge genome and I have produced the genomescope plot from the 21-mer kmer frequencies. I have hard time interpreting the plot. Can someone please help me?
Thank you.
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Trimmomatic QC report shows drop in the reads and presence of overrepresented sequences
This question was also asked on Biostars
I am performing a de novo genome assembly using Illumina paired-end short reads, sequenced on a NovaSeq X by our collaborator at UCLA.
At present, I am in the ...
5
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How to get cytoband and gene level copy number from genome wide SNP array copy number data?
I have (human) Illumina genome wide SNP array copy number data. For each SNP genomewide, I have Log R Ratio (LRR) and B Allele Frequency (BAF).
What tool(s) can I use to get the integer copy numbers (...
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