Genetics

Scientist, Next Generation Sequencing (Molecular Biology) at Flagship Pioneering, Inc. Cambridge, MA USA Company Summary: Flagship Labs 72, Inc. (FL72) is a well-funded, early stage biotechnology company founded by Flagship Pioneering that is developing a new category of immune therapeutics. FL72 was founded through Flagship’s venture creation engine, where companies such as Moderna Therapeutics (NASDAQ: […]

I have a count matrix from an RNA-seq experiment that I’d like to normalize using DESeq2 and perform DE analysis on. My code is below: dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design= ~ condition) My experiment is performed over two time periods, week1 (with treated vs untreated) and week2, (untreated vs untreated). Samples […]

Caribou Biosciences, Inc., a Berkeley, California-based CRISPR genome-editing biopharmaceutical company, raised $304M in an initial public offering, one of the most lucrative IPOs in gene-editing. In June 2021, Gene editing biotech Verve raised $267M in IPO proceeds and later added another $40 million after its financial underwriters opted to buy more shares, bringing its gross […]

Local blast database 0 I tried to use a “update_blastdb.pl” perl skript to build a blast database locally. I ran update_blastdb.pl –decompress refseq_protein but got this error . What do you think about it? Best regards! database update_blastdb.pl blast • 125 views Login before adding your answer. Source link

how to Seurat::RunUMAP() but run reduction=”pca” on subset of features? 0 How can I run umap on a seurat object, and specify the features (genes) to use for the initial PCA reduction? I’m looking for something like what the following [hypothetical] syntax would achieve: data(“pbmc_small”) pbmc_small # Run UMAP map on first 5 PCs pbmc_small […]

Pooling annotations from different databases in InterProScan 1 Is it acceptable to pool the annotations from the various sources InterProScan offers, and annotate a sequence with a subset of these? For example, if I have something like so: id annot src start stop seq1 dom1 Pfam 100 120 seq1 dom1a CDD 101 128 seq1 dom2 […]

Problems with fragment length distribution output with Salmon 1 Hi all, New to RNA-Seq and I’m struggling with my Salmon alignment output. I tried to find an answer to this question on older posts but I couldn’t locate any other discussions, so apologies in advance if this has been covered before. My data is from […]

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Research Associate in Computational Biophysics, University of Manchester Job reference: BMH-017047 Location: Oxford Road, Manchester, UK Closing date: 19/08/2021 Salary: £32,816 per annum Employment type: Fixed Term Faculty/Organisation: Biology, Medicine & Health School/ Directorate: Molecular & Cellular Function Hours per week: Full Time Contract Duration: 01 August 2021 until 31 July 2024 This is a […]

Read group info 0 Hello I need help in getting read group info for performing alignment using BWA-MEM2. I read previous post (bwa mem: Passing a variable to read group) on read-group info, where a shell script is used to get the read group info from fastq file. Can someone explain what details should be […]

I wrote a script on how to analyze the microarray-based miRNA expression data. Here is my code: # general config baseDir <- ‘.’ annotfile <- ‘mirbase_genelist.tsv’ setwd(baseDir) options(scipen = 99) require(limma) # read in the data targets <- read.csv(“/media/mdrcubuntu/46B85615B8560439/microarray_text_files/targets.txt”, sep=””) # retain information about background via gIsWellAboveBG project <- read.maimages(targets,source=”agilent.median”,green.only = TRUE, other.columns = c(“gIsWellAboveBG”,”gIsSaturated”,”gIsFeatPopnOL”,”gIsFeatNonUnifOL”) […]

Using joiningdata/lollipops to make lollipop chart 0 I’m having trouble downloading and using pbnjay’s lollipop I went and downloaded the mac version and opened up “lollipops” in the command line. I closed the terminal and then opened it again, and tried: lollipops TP53 R273C R175H T125 R248Q but go the following error: -sh: lollipops: command […]

clusterProfiler and enrichplot: visualising groupGO results with individual genes and their fold changes 2 Hi, I’m using the groupGO command in clusterProfiler to group a subset of (e.g. significantly DE) genes under GO terms. I would like to visualise the results where the relationship between the GO terms, the genes, and their fold changes are […]

Determine where an interleaved FASTQ record starts 0 FASTQ-files have a record length of 4 lines. But you can also determine where a record starts even in the middle of a file by looking at ‘@’ and lines around that (see stackoverflow.com/a/41707920/363028). Can we do something similar with interleaved FASTQ-files? Based on stackoverflow.com/a/68707816/363028: is there […]

In another boost to India’s vaccination, sources on Monday, said that Zydus Cadila’s vaccine ZyCov-D’s approval will occur in this week. Zydus Cadila applied for Emergency Use Authorisation (EUA) for ZyCoV-D on July 1, after the completion of the third phase of trials. The Ahmedabad-based company which has developed the world’s first DNA COVID-19 vaccine, […]

Variant calling from 5 MB regions coming from contrasting cultivars 0 Hi, I would like to compare ~5 MB genomic (QTL) regions across two groups (resistant and susceptible) and identify variants that might majorly influence resistance. I was thinking of the following pipeline; use susceptible cultivar as the reference (since there is only one) Assemble […]