I got my genome sequenced to help my dad with a genealogical brick walI (still no luck). What else can I do with it (cancers/diseases/phenotypes)? I don’t know much about genomics, but I have a good PC and can use CLI tools. The data is 2 files (60 GB each) of FASTQ. I have a BAM file that I’ve aligned to GRCh38. (Any point in aligning to CHM13?) I also have various VCFs. submitted by /u/Ambitious_Cup6896 [visit reddit] [comments ..read more

Hello, I am new to Bioinformatics and coding as a whole. My degree is in biology and I am almost done with my associates. I created a phylogeny a few weeks ago using maximum likelihood method. To go into more detail about the programs and methods I used, here is a short outline. Sampled 46 specimens and extracted DNA use QIAGEN DNeasy Blood and Tissue Kit. Used Illumina to sequence genomic data, used Hybpiper and MAFFT with the auto option for assembly and alignment. Inferred a tree with IQ-TREE 2 and visualized the tree with FigTree. My next goal is to create a tree using Bayesian method. Is ..read more

Hi, I've been using the CellOracle tool to infer Gene regulatory networks from my single cell RNA seq data. I have inferred the GRN models and i have obtained the network results as a list with source, target, coef_mean, coef_abs, p, -logp values. I want to use this list to visualise my network on cytoscape. How can I achieve this? Which app on cytoscape should I use? Can someone please please help me out? submitted by /u/Evening-Ad7435 [visit reddit] [comments ..read more

Hello everyone, I have run a blast using the 'blastn' and have received a table gathering all the Accessing number and taxonomic identifier from my sample. I was wondering if there was a way of retrieving the family, species, phylum etc from this using bash and putting it in a tab so that I can know the actual identity of my sample. thanks, submitted by /u/smartise [visit reddit] [comments ..read more

I am looking for a tool which can draw synteny between two sequences with certain regions masked. This is a bacterial genome and it has many phage (complete or fragmented) inserted throughout the genome. I would like to mask all the bacterial regions (90 % of the sequence) and draw synteny with reference phage genome. I am new to drawing synteny. If there is any tools or pipeline that is known for this, please share. ​ Thanks in advance submitted by /u/Klutzy-Pollution3519 [visit reddit] [comments ..read more

hi, i am a molbio person from wetlab field but i felt a little courage to get a sequencing class this sem. to pass it, we need to make a project with using bulk rna-seq data and complete everything on school's cluster. first, i wanted to work on microbiome, but the lecturer didn't like the idea. most of the friends tried to build on something from encode database, so i went with the flow, i chose immune cell seq data from bernstein lab's research. basically, what i wanted to do is looking expressional differences on some particular protein at healthy vs ms people. like i said, i am so wet beh ..read more

Hello! My name is Gauri and I am currently nearing the end of my 11th grade. We have this research project called an Extended Essay and I have chosen to do it around the use of CRISPR-cas9 as a therapy for sickle cell anaemia. Ironically, this "essay" is actually to be an experiment and hence if I want to proceed I would need to use computational models. According to research, a custom adenine base editor, namely ABE8e-NRCH has been used to convert the pathogenic allele to a makassar non pathogenic variant. Is there any platform that can allow me to test out this modified CRISPR-cas9 online f ..read more

If I google Nblast I used to just click the first link and be on my way, now it takes so much longer. Can't even write NCBI Nblast, you have to be fully verbose. Worst change ever. submitted by /u/UNSWNerd [visit reddit] [comments ..read more

I tried google but nothing comes up. submitted by /u/BiggusDikkusMorocos [visit reddit] [comments ..read more

The above. submitted by /u/BiggusDikkusMorocos [visit reddit] [comments ..read more