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We would like to verify whether there is a significant difference in efficiency of the hm pipeline for seq GWAS.
1. Calculate the average % of dropped and unable to harmonise variants among a repres…
ljwh2 updated
6 months ago
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I want to ask if there is any possibility of using WHATSHAP for phasing my dataset which consist of Illumina whole genome sequencing at high coverage using also long reads from PacBio and Nanopore.
I…
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I am interested in structural variants/copy number variants (SVs/CNVs) of whole genome sequencing data of patients with Epilepsy, but I do not know where to commence with the analysis once the output …
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Recently, U.S. Food and Drug Administration, National Institute of Standards and Technology and Illumina [researchers defined highly reproducible regions (H.R.R.s)](https://genomebiology.biomedcentral…
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Do you think centrifuge would be successful at classifying 16S reads from Oxford Nanopore? The nanopore reads cover the entire 16S gene (1522bp) but have a high error rate (10-15%). Have you tried …
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Whole-genome sequencing of S. paradoxus mutation accumulation lines
DNA extracted using Zymo YeaSTAR Genomic DNA kit
Libraries prepped using homemade protocol (no kit, can find out more info if ne…
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Hello, Dr. Ahn,
I recently applied TenSQR to reconstruct quasispecies on whole genome sequencing data from a virus sample (>20000X, 150bp paired end, Illumina). TenSQR outputted 10 quasispecies seq…
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"Whole-genome sequencing and targeted amplicon capture" says:
> "Do not mark duplicates in the BAM files for samples sequenced by this method"
However, in the BAM file preparation, it is writt…
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I mapped whole genome sequencing data using the `-a` option. Some alignments have a Flag total of 377 and 441. According to Explain SAM Flags internet tool, 377 includes mate unmapped, read reverse s…
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