User: nickeener

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nickeener20
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Posts by nickeener

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Comment: C: How to Detect Frameshifts in a Protein Alignment
... This is what I ended up doing. But thank you for verifying that this method is sound. ...
written 6 weeks ago by nickeener20
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Comment: C: How to Detect Frameshifts in a Protein Alignment
... Thanks for the answer! What I'm really trying to do is write my own translation aligner similar to the TranslatorX tool that you mentioned but with some additional features. So if possible I would like to do this without adding another tool dependency. So what I need is a method to detect a frameshi ...
written 6 weeks ago by nickeener20
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How to Detect Frameshifts in a Protein Alignment
... I'm performing multiple alignments on a series of protein sequences but I want to throw out any sequence that has a frameshift mutation compared to a reference sequence. I'm starting with in-frame genes which are then converted into their amino acid sequences. My original idea was to simply run a lo ...
mutation sequence alignment detection frameshift written 6 weeks ago by nickeener20 • updated 6 weeks ago by Mensur Dlakic4.1k
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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 5 months ago by nickeener20
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Comment: C: Large Discrepancy Between Short Read Mapping and Kmer Analysis
... HowDeSBT (https://github.com/medvedevgroup/HowDeSBT) ...
written 6 months ago by nickeener20
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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 6 months ago by nickeener20 • updated 6 months ago by genomax80k
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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 months ago by nickeener20 • updated 4 months ago by Biostar ♦♦ 20
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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 13 months ago by nickeener20 • updated 13 months ago by darren.obbard20

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