Hi all, I am working on a gwas and I need some advice on early data qc and processing. I’m reading a lot but there is still some “experience gap in knowledge” - [advisors are not knowledgeable or helpful] The data from illumina is made up of 3 batches (there are some batch control duplicates included in 2 and 3). Each batch has multiple illumina reports GSGT files (as *.cvs.gz). 1) my plan is to convert the reports to a plink supported format, then merge them into 1 file for the batch. Is that the right approach? 2) next, I planned to do the QC on each batch, and impute each batch separately ..read more

Hello! This is (hopefully) a quick question, but as a non-bioinformatics person who just received g.vcf.gz.tbi files, how do you open them? I have no idea which program to use. Thanks! submitted by /u/GoodnightMoose [visit reddit] [comments ..read more

Hi! I'm a sophomore majoring in Microbiology at the moment. I'm enjoying it, but I've been thinking of a major at my school called Genomics and Molecular Genetics at my school. The reason I want to switch is because I recently picked up a minor in anthropology, which is a major interest of mine, and my dream is to work biological anthropology research, broadly. I'm going with the flow... currently I'm working in a mosquito research lab until I find a lab where I can shadow in biological anthropology. I do not wish to work in anything medical, and it seems like thats my only option if I stay i ..read more

Also included on report: “This assay contains a limited number of loci for which more than one pathogenic variant has been reported in the affected population (rs5742904, rs80357701/rs80357089, rs80358150/rs273901754, rs80359876/rs80357390, rs80359883/rs41293465, rs80359380/rs80358573, rs76173977, rs139624145, rs145787161, rs267608076/rs63749874, rs387906397, rs267608153, rs267608154/rs63750544) and the current technical platform version cannot reliably distinguish which of the pathogenic variants is present.” submitted by /u/Overitwisconsin [visit reddit] [comments ..read more

submitted by /u/gwern [visit reddit] [comments ..read more

I am wondering how a methyl group could be added and what it could do. I don't have background in science. Thanks submitted by /u/wannabehedgefun [visit reddit] [comments ..read more

I was tryna blast TERC gene in humans and zebrafish - unable to get any results on blastn while clustal omega gives an output for the alignment. I could get results with TERT gene - did I download the wrong sequence files or what am I doing wrong? Ensembl didn't have TERC for Zf and i downloaded from NCBI - Danio rerio non-coding telomerase RNA gene, complete sequence Sequence ID: EF569636.1 Length: 317 Number of Matches: 1 and Homo sapiens telomerase RNA component (TERC), telomerase RNA Sequence ID: NR_001566.1 Length: 451 Number of Matches: 1 submitted by /u/Mendelianne [visit reddit] [com ..read more

We recently developed a deep learning algorithm that can diagnose a rare disease from a medical imaging source (cardiac MRI). Now, I am thinking about running this model on all patients from All of us and Biobank, find the patients with disease. Until here, it is simple. The next part is tricky for me and don’t know how should I do it. After finding patients with disease, I would like to compare them with patients without disease and find new genetic features associated with that disease. How would one do this? What should I learn to be able to do this? What should I expect from my attempt to ..read more

Are there any NP-complete and NP-Hard ones? submitted by /u/Seven1s [visit reddit] [comments ..read more

I'm working with dna sequences, classifying them into species using Deep Learning Methods, I don't have any background in biology or any knowledge for genomics. I had a one question, currently I have a dataset that has 70,000 sequences each of 1000 nucleotides length. These are for 9 different covid variants and my task is to classify them accordingly, if for example I take a sample sequence of 1000 nucleotide length that belongs to species 1 and chop it into 10 sequences of 100 length each, could I say that this fragment would also belong to species class 1? does that work? or there needs to ..read more