I am a senior in college majoring in health informatics. I have extremely limited research experience and would love to get started. How do I go about that? Should I just randomly email professors/ schools whose research I’m interested in? Or do I need a direct connection to them? What’s the best way to network? Should I try conferences? What are the certifications most sought after in the field? Has anyone worked at the NIH? What’s your job title/ salary? I would love if anyone could answer any of these as I feel like a fish out of water. Thank you! submitted by /u/RevolutionaryEdge959 [vis ..read more

Hi all, I have 3 groups with 3 isoform of a gene: A (protective), B (normal) and C (risk). 2 isoforms (A and B) have normal phenotype and isoform C has high risk of disease. I would like to find pathways behave differently between isoform A and C. Currently I use GSVA (gene set variation analysis) to get pathway score then use these pathway score to build linear model: pathway score ~ isoform + covariate. I filter pathway that have opposite beta between 2 isoforms. Another method I tried is gene set enrichment analysis. Would you recommend a method or paper has similar question? Do you think ..read more

I'm trying to check if my matrix is all right, but in the end of the code I have to change "mcmc" to "mcmcp", and it's not working, the program show an error on the "mcmcp" line, do anyone already have this problem or know how to solve it? submitted by /u/Cursewill [visit reddit] [comments ..read more

-i have 3 group of RNAseq samples, let's call them group A, B, C. -i have performed DESEQ on A vs C, and B vs C. (it make sense biologically) -then I look at the shared DEGs between both comparisons and make conclusions based on the shared DEGs. my question is: does compared A and B to C bias my data? submitted by /u/snoop_pugg [visit reddit] [comments ..read more

Hello all, recently I have become fascinated with bioinformatics and have some questions for the pros here. I have my BS in CS and 6 years of software engineering and data engineering experience. I am working on my masters in CS with a focus on ML from Georgia tech (online) right now. Over the past few months I have decided that I don’t want to be a SWE forever and want more of a purpose to my career. I want to be a bfx scientist and do cancer research. Here is the problem. I have ZERO, and I mean ZERO, biology, o-chem, or any other life science courses/experience. I have a purely CS backgrou ..read more

Hi there, I'm just wondering if anyone has any experience assembling really huge and diverse reads data and what are the tools or parameters you used to optimise the process? I have some deep sequenced soil samples (100 million+ reads per sample, 4 lanes of reads for each sample). The issue is contig length. Using spades I'm getting a maximum contig length of 50kb which just seems hopeless since bacterial genomes can be millions of bp in length. Running quast on a sample showed I had 9 contigs > 10,000 bp ☠️. Wtf?! Megahit is not much better despite providing the parameters to specify that ..read more

Hello once again! Recently I developed a project in MatLab for biological sciencies, very basic stuff, and thought it was super useful for simulating tissue and protein dynamics. I don't know if it is still bioinformatics or is it more pure computational science / engineering, but is it worth taking a deeper dive into MatLab if I currently have a spot as a bioinformatician? or is it just wasting time? I'm solid at R and know a bit of Python. submitted by /u/Vegetable_Past_9819 [visit reddit] [comments ..read more

Hey everyone, hopefully y'all are doing good. So I've this issue, I designed primers for my gene whose size was large, so I divided the gene into 4 fragments and made overlapping primers. Now, for template I used two cDNA samples. So, I'm not getting PCR product for fragment 1,3 and initially I got product for fragment 4 by both cDNAs, however for 1 cDNA the band was quite sharp and for other it existed but a bit light. Now I'm again using the light one cDNA template for amplification of fragment 4 and even the profile is same as I used for first amplification. But now I'm productless, so idk ..read more

Hello everyone, I am a biostatistician epidemiologist, with some knowledge in bioinformatics, I have to relay a methylation analysis from FASTQ files. Is it possible to do this analysis from FASTQ files? If so, could you recommend me an R package for this purpose? I would be grateful for any information). Many thanks for considering my request. submitted by /u/Yassir_med [visit reddit] [comments ..read more

I have generated .narrowPeak files using genrich and I am trying to run DiffBind to understand differential accessibility analysis. for my samplesheet, does there have to be a bamfile or do I use .bw file with a bigWig column in my sample sheet since the bw file was created using bamCoverage and normalised RPKM. what steps should i follow next? I am new to NGS data analysis and would really appreciate help! I thought I could use the bigwig files instead of the bamfiles so that the dba.count method can work? ​ submitted by /u/Other-Corner4078 [visit reddit] [comments ..read more