User: ravihansa82

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ravihansa8270
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Posts by ravihansa82

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Comment: C: Variation in SNP calling
... Hi JC, Thanks for the reply. May be silly things to ask. You mentioned that the variants calling for G2 is not useful. Is it due to the small genome size compared to G1? ...
written 3 months ago by ravihansa8270
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Variation in SNP calling
... Hi, I have NGS DNA sequence reads for two different plant species (A and B) in the same genera. I did sequence alignment of species A for its reference genome(G1) found for example 10000 SNPs. However, species B doesn't have a reference genome. Therefore, I selected a genome (G2), which is closely r ...
alignment next-gen snp written 3 months ago by ravihansa8270
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problem in vcf to genlight conversion
... Hi , I have a file with snp data in vcf format. I need to do population genetics studies. Therefore, I installed the Adegenet package into R. Also I installed the vcfR package as well. I read the vcf file as My_vcf<- read.vcfR(). then I tried to convert imported vcf file to genlight as vcf_gl < ...
software error R next-gen snp written 4 months ago by ravihansa8270
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In silico protein modeling
... Hi all, I am currently working in protein - protein interaction. One of my objectives was to identify the interaction domains of those two proteins. Luckily I found the interaction domains. One of those two proteins is a novel protein. There was no homology sequence found so far. Interestingly, tha ...
genome assembly gene written 15 months ago by ravihansa8270 • updated 15 months ago by Mensur Dlakic7.3k
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Comment: C: RNA seq data shows no gene expression but qPCR shows the same gene is upregulate
... hi Kristoffer, I aligned the sequence reads to the target chromosome. finally, I found sequence reads align with the target chromosomal region. thanks a lot for your suggestion. ...
written 15 months ago by ravihansa8270
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Comment: C: RNA seq data shows no gene expression but qPCR shows the same gene is upregulate
... Hi Shawn, what I understood from the Bioinfomatician, he gave me a list of ensemble gene IDs with the number of read counts for indivudual genes. in that data there were many genes showed as 0 reads. in that 0 gene list I found one of the universal known gene read counts also 0. when I do qPCR for t ...
written 18 months ago by ravihansa8270
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RNA seq data shows no gene expression but qPCR shows the same gene is upregulated
... Recently I did RNA sequencing using ovarian tissue samples to find out the differencial gene expression in ovary based on WT and mutant gene. Bioinformatics results analysis show one of the gene expression is 0. However, when I do qPCR for the same gene I can see upregulation of that gene in several ...
gene next-gen rna-seq written 18 months ago by ravihansa8270 • updated 18 months ago by kristoffer.vittingseerup3.4k
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Transcript Specif qPCR primer
... I have a gene which is having 10 transcript variants. However, only 4 transcripts are protein coding ORFs. I need to find out the level of expression of only one transcript out of 4 protein coding transcripts. I used NCBI Primer blast tool to design qPCR primers. however, designed primers not only d ...
genome gene written 21 months ago by ravihansa8270
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(Closed) DAAD Interview Questions
... Dear Friends, I have selected for daad scholaship and they will invite me for the interview coming days. if some one who has already faced such please share how was the interview and what type of questions they asked during the interview ...
off-topic written 4.9 years ago by ravihansa8270 • updated 4.9 years ago by Michael Dondrup48k
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[BIOINFORMATICS?] Compare two methods
... Dear Friends I am going to analyze a new way of processing of pathological samples for microscopic examination compared to the conventional method. I am going to look for, microtony characteristics(V1), mounting characteristics (V2), etc. for each I will give a score varying from 1 to 3(1 = poor ,2 ...
R written 5.0 years ago by ravihansa8270 • updated 5.0 years ago by _r_am31k

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Appreciated 15 months ago, created a post with more than 5 votes. For Why am I getting different ensembl gene ids for a given gene symbol?
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