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 “” perl skript to build a blast database locally. I ran –decompress refseq_protein but got this error . What do you think about it? Best regards! database 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 […]

Latest business intelligence report released on Global Minichromosomal Technology Market, covers different industry elements and growth inclinations that helps in predicting market forecast. The report allows complete assessment of current and future scenario scaling top to bottom investigation about the market size, % share of key and emerging segment, major development, and technological advancements. Also, […]

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 Can we do something similar with interleaved FASTQ-files? Based on 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 […]