User: nickeener

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nickeener0
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Posts by nickeener

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Can someone explain what F1R2 and F2R1 counts mean?
... I'm doing variant calling using GATK4's Mutect2 and trying to filter variants based on strand bias and other metrics and I feel like the F1R2 and F2R1 counts would be useful in this but I'm not entirely clear on what they mean. I understand that F1R2 is the number of first pair reads that mapped to ...
variant calling f2r1 f1r2 mutect2 written 2 days ago by nickeener0
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Comment: C: Large Discrepancy Between Short Read Mapping and Kmer Analysis
... HowDeSBT (https://github.com/medvedevgroup/HowDeSBT) ...
written 4 weeks ago by nickeener0
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Large Discrepancy Between Short Read Mapping and Kmer Analysis
... Hi all, I'm working on a project that involves trying to develop a method for identifying whether a specific sequence (specifically looking at viral genomes) is contained within short-read sequencing data or not. I'm using this tool that creates a searchable index of all kmers that occur more than t ...
short-read mapping kmer counting written 5 weeks ago by nickeener0 • updated 5 weeks ago by genomax73k
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How to get individual strand counts from Mutect2 for multi-allelic sites
... Hi all, I'm trying to pull strand count information from a VCF file made using GATK4's Mutect2. I used the following command to create this VCF: gatk Mutect2 -I SRR8525881.bam -mbq 20 -R ../../genome/hxb2.fa --mitochondria-mode True -O SRR8525881.vcf The VCF output for multi-allelic sites look ...
gatk4 vcf mutect2 written 6 weeks ago by nickeener0
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Finding Reads from a DNA Virus
... Hi, I'm trying to locate viral reads from a DNA virus in Drosophila sequencing data from NCBI's SRA and was unsure whether using RNA-seq experiments would be productive or not. Obviously the virus must transcribe its DNA into RNA in order to have its viral proteins translated, but my question is: si ...
sra virus detection rna-seq written 7 months ago by nickeener0 • updated 7 months ago by darren.obbard20

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