User: tmrhyd

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tmrhyd0
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Posts by tmrhyd

<prev • 23 results • page 1 of 3 • next >
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Whats the Difference between variants and SNPs in IGV?(or in general)
... I have a VCF file and a Bam file in IGV and am trying to find out what variants are have the loudest signal by lining up the variant mark given by the VCF track to the colored base line in the .bam coverage track. Does this sound like it is the right way to tell if something is the best SNP/Variant ...
gene genome written 2 days ago by tmrhyd0 • updated 2 days ago by RamRS22k
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Comment: C: How to annotate chloroplast genome with a .gff file of the entire organism?
... I aligned my chloroplast reference Fasta against the genome of a modified version of my original plant, and now have the VCF of that vs the original plant genome aligned against the same chloroplast reference fasta. I have the .gff that has all the annotations for the entire original plant genome an ...
written 5 days ago by tmrhyd0
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How to annotate chloroplast genome with a .gff file of the entire organism?
... Hey all, I know some of my past posts haven't made too much sense, so I hope this makes sense. I have a .gff file with the annotations for the entire genome of my plant species, and I want to use it to annotate just the chloroplast genome. How do I extract or apply just that part of the .gff file ...
gene written 5 days ago by tmrhyd0
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Comment: C: What should I use to annotate the plant genes for a VCF or a Fasta?
... Does the fact that each sample has hundreds of variants not provide the data set for the statistical test to get the P data and therefore the Manhattan plot? Thank you so much for your help!! ...
written 6 days ago by tmrhyd0
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Comment: C: What should I use to annotate the plant genes for a VCF or a Fasta?
... No, I honestly need a guide or basic overview. I'm really lost and just trying to get Manhattan plots from the data given to me. Do you know of any good resources for a basic overview on the genomics pipeline creation process? I am so sorry about the wording of my questions, I didn't know how else ...
written 6 days ago by tmrhyd0
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What should I use to annotate the plant genes for a VCF or a Fasta?
... I have a Fasta and a VCF of a plant genome, for sequence A and sequence B. Sequence A is the Wildtype, and sequence B is an improved mutated version of it. I have been comparing the variants of the two sequences in IGV, but need to annotate the genes. I have the variants annotated with snpEff, but I ...
genome R snp gene written 6 days ago by tmrhyd0
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Comment: C: SnpEff annotation keeps throwing Java Errors
... That worked! thank you!! ...
written 9 days ago by tmrhyd0
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SnpEff annotation keeps throwing Java Errors
... So I keep running the following code. snpEffBuildAndRun --snpeff-exec /home/treinbo/snpEff/snpEff.jar KMM.gff 6_KMM7_Chloroplast_freebayes_07012019.vcf -o 7_KMM7_chloroplast_annotate.vcf And it keeps giving me the following error. Traceback (most recent call last): File "/home/t ...
genome assembly snp written 10 days ago by tmrhyd0
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How to subtract out wildtype variants, and what is it?
... I have Bam files, sorted and indexed, and VCF files, and was told that I need to subtract the wildtype variants out of my files, and to use VCFtools or Freebayes. What is subtracting out the wildtype variants? How do I do it? Since I have VCF files is it already done? Thank you all so much!! ...
genome assembly snp written 11 days ago by tmrhyd0
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Comment: C: What is " dbSnp132.vcf " in the snpEff tutorial?
... So I can't use snpEffs annotation function for algae? What should I use to annotate the VCF file I have? Thank you so much!!! :) ...
written 13 days ago by tmrhyd0

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