User: rtyb91

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rtyb9120
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Posts by rtyb91

<prev • 9 results • page 1 of 1 • next >
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Downloading canine annotation in Annovar for SNP detection possible?
... Dear community members, I am currently trying my luck with the tool called ANNOVAR in my attempt to filter out my huge data of SNP called from the whole genome sequencing of 3 dogs after SNP calling and filtering using a commercial product named Strand-NGS. I realized there are multiple studies ou ...
next-gen snp sequencing written 4 months ago by rtyb9120
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Comment: C: Mapping canine whole genome sequencing to camfam3 reference genome on BWA-MEM
... Hmm, I wonder where the FASTA file chunk of the CanFam3.1 went to. I will dig it up soon! I see, so you would recommend running the samples on clouds instead! Will that be efficient for a dual boot Windows with quad core and 16GB RAM? ...
written 4 months ago by rtyb9120
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Comment: C: Mapping canine whole genome sequencing to camfam3 reference genome on BWA-MEM
... Thanks for the tips Igor! Now I need to find a way to convert the files to FASTA format instead. As for running WGS on single desktop machine, if you were to advise against it, may I ask for some suggestions to how should I approach this? Thank you! ...
written 4 months ago by rtyb9120
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Mapping canine whole genome sequencing to camfam3 reference genome on BWA-MEM
... Dear Community, I am trying to detect variants in a specific breed of dog where we hypothesis the variants may be involve in the pathogenesis of a certain disease. With that aim, we performed whole genome sequencing of 3 unrelated dogs with the disease, and plan to compare the sequencing of these s ...
ngs whole genome sequencing snp written 4 months ago by rtyb9120 • updated 4 months ago by igor11k
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Comment: C: DNA-Seq and Whole Genome Sequencing, are they the same?
... Thank you for the clarification! That clears the air immensely! Sorry for being such an amateur though, some how google searching and reading heaps of articles couldn't answer this question. ...
written 5 months ago by rtyb9120
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DNA-Seq and Whole Genome Sequencing, are they the same?
... Dear members, I have currently dispatched an order for whole genome sequencing in dogs using DNA extracted from whole blood using Qiagen DNEasy kit, and I was reading through publications to prepare for my analysis when the results return. One question I have always gotten from my senior was what ...
genome dna-seq whole genome sequencing written 5 months ago by rtyb9120 • updated 5 months ago by ATpoint38k
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Answer: A: DEG using edgeR script via StrandNGS
... Just to wrap things up, I finally got in touch with the StrandNGS tech support (actually they came to me first) and we managed to sort things out to proceed with more discussion via emails and zoom. Their tech support is amazing and I do recommend StrandNGS users to get in touch with then directly t ...
written 8 months ago by rtyb9120
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Comment: C: DEG using edgeR script via StrandNGS
... Thanks for the input! I'm really trying my luck here because the accession I have is from Japan, and the support I likely to have would be in Japanese. While I am fairly well-versed in the language, I would really prefer support and inputs for the analysis in English so I wouldn't have any misunder ...
written 8 months ago by rtyb9120
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DEG using edgeR script via StrandNGS
... Dear All, I am a veterinarian working on a breed-specific disease with limited number of samples sent for RNA-Sequencing. As I was told that I am a biologist instead of bioinformatician, I was directed to use the commercial product StrandNGS to run analysis on my sequencing results. There is a tut ...
R rna-seq written 8 months ago by rtyb9120

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Scholar 8 months ago, created an answer that has been accepted. For A: DEG using edgeR script via StrandNGS

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