Categories
Tag: Salmon
Sperm-specific histone H1 in highly condensed sperm nucleus of Sargassum horneri
Cho, C. et al. Haploinsufficiency of protamine-1 or-2 causes infertility in mice. Nat. Genet. 28, 82–86 (2001). Article CAS PubMed Google Scholar Oliva, R. Protamines and male infertility. Hum. Reprod. Update 12, 417–435 (2006). Article CAS PubMed Google Scholar Balhorn, R. The protamine family of sperm nuclear proteins. Genome Biol….
Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout
FAO. The State of World Fisheries and Aquaculture 2022: Towards Blue Transformation (FAO, 2022). Google Scholar Hua, K. et al. The future of aquatic protein: Implications for protein sources in aquaculture diets. One Earth 3, 316–329 (2019). Article Google Scholar Hardy, R. W. Utilization of plant proteins in fish diets:…
Batch and Sample correction for downstream analysis using DESeq2
Hello everyone, I am an absolute beginner on sequencing analysis and DESeq2, so please forgive me for possibly mundane questions. I have tried to look up different methods, but couldn’t find a fitting answer yet. I am currently working with sequencing data derived from an Illumina sequencer. The data is…
Archaic Introgression Shaped Human Circadian Traits | Genome Biology and Evolution
Abstract When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in…
Plot and table in R-studio
I want to make a model and plot that shows how long it takes for salmon lice to lay eggs and how the time differ between wild and farmed salmon lices. Then I want to make a table or paragraph that uses the plot. I tried to use Phind to…
downstream analysis on the output of nf-core/rnaseq pipeline
downstream analysis on the output of nf-core/rnaseq pipeline 1 Hello everyone, I ran nf-core/rnaseq pipeline successfully, now I want to do downstream analysis like machine learning on the generated output files from this pipeline. Should I use salmon.merged.gene_counts.tsv for that and apply log transformation to normalize it before doing downstream…
Correlation methods giving very different results (WGCNA)
Hi all, I’ve come back to WGCNA after some years and have run into a bit of a quirky result when looking at my soft power thresholds depending correlation the methods I use. Generally, this topic has been discussed a fair bit – but was looking to see if anyone…
Alternative to Gentrome?
Alternative to Gentrome? 0 For context, after running the salmon index line, the process is killed after clipping some poly-A tails. However, I don’t have access to a higher computer, and I currently run on my ASUS G14 with 16.0 GB RAM, and 500gb of hard drive space. salmon index…
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
Hi all, I am running WGCNA on my big gene expression data set, and running into a bunch of errors. I appreciate any help in advance that you can provide in navigating these! First, the graph generated to choose the power is wacky looking. I chose 28, as I figured…
B.C. scientists scooping killer whale poop to search for DNA – BC
Scientists at the Raincoast Conservation Foundation are sifting through killer whale poop to search for DNA that will shed light on the health of their populations, individual specimens and the ecosystems they live in. The work is underway at what the foundation describes as a “cutting edge” genetics lab at…
Why claims of a new ‘genetic vaccine’ being given to Australian children don’t align with reality
CheckMate December 8, 2023 This week, we debunk viral social media posts that claim a new “genetic vaccine” has been added to the national vaccine schedule for children aged 2-6 months. We also show why the “mother of all revelations” was more fizzer than Pfizer, and identify some of the…
Electric Eels Have a Special Genome That Allows Them To Produce Electricity, Researchers Find
Electric eels are known for their ability to generate powerful electric shocks that can stun their prey and deter predators. But did you know that they can also help scientists create genetically modified fish? A recent study has shown that electric organ discharge from electric eels can facilitate DNA transformation…
Salmon indices differences
Salmon indices differences 1 I am trying to run Salmon locally on prostate cancer samples, and I used this command: salmon quant -i data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/salmon_sa_index/default -l A -1 SRR21898893_1.fastq.gz -2 SRR21898893_2.fastq.gz –validateMappings –gcBias -o transcripts_quant I downloaded the pre-built versions of the partial decoy (salmon_partial_sa_index) and full decoy (salmon_sa_index) indices from…
DEseq2 input
DEseq2 input 1 Hello Guys, @Michael Love I have a transcriptomics dataset and did rnaseq/nf-core pipeline by salmon-star. my output of the salmon-star folder is as follows: salmon.merged.gene_counts.tsv salmon.merged.gene_counts_length_scaled.tsv salmon.merged.gene_counts_scaled.tsv salmon.merged.gene_lengths.tsv salmon.merged.gene_tpm.tsv salmon.merged.transcript_counts.tsv salmon.merged.transcript_lengths.tsv salmon.merged.transcript_tpm.tsv tx2gene.tsv my question is: which one of these files should be an input for Deseq2…
Best practices for unstranded sequences in featureCounts
Hi everyone, I’m using featureCounts to analyze some RNA-Seq data, but I have several doubts in the use with unstranded library. First, when I analyze some SRA sequences or when I don’t know the library type, I use Salmon to know it with the next command: salmon quant -p 32…
Salmon index problem
Salmon index problem 0 Hello, I’m trying to use Salmon in the mapping-based mode, and I downloaded the full decoy salmon indices via refgenie list here using the refgenie command refgenie pull hg38/salmon_sa_index and it download the full folder locally. Now I have this index folder and SRR21898893_1.fastq.gz and SRR21898893_2.fastq.gz…
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
Hello all, Background: I’ve inherited a new RNAseq data set and am thinking about updating my approaches (last time I did this I was using HISAT and Cuffdiff). I’d like some opinions on best strategies to disentangle/filter out parasite microbe reads from infected host reads before preforming a differential gene…
Shotgun metagenomes from productive lakes in an urban region of Sweden
Williamson, C. E., Saros, J. E., Vincent, W. F. & Smol, J. P. Lakes and reservoirs as sentinels, integrators, and regulators of climate change. Limnology and Oceanography 54, 2273–2282, doi.org/10.4319/lo.2009.54.6_part_2.2273 (2009). Article ADS Google Scholar Cavicchioli, R. et al. 2019. Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews…
Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient
Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA. 103, 626–631 (2006). Article ADS CAS PubMed PubMed Central Google Scholar Gao, C. & Guo, L. Progress on microbial species diversity, community assembly and functional traits. Biodivers. Sci. 30, 22429 (2022)….
salmon for gene expression quantification
salmon for gene expression quantification 0 Are the results of salmon reliable for gene expression quantification? Because it just gives gene expression in terms of TPM and Number of Reads by just one command taking input as fastq files. salmon gene-expression • 62 views • link updated 8 minutes ago…
KEGG T09424: 118385109
Entry 118385109 CDS T09424 Name (RefSeq) adenylosuccinate synthetase isozyme 2-like KO K01939 adenylosuccinate synthase [EC:6.3.4.4] Organism oke Oncorhynchus keta (chum salmon) Pathway oke00230 Purine metabolism oke00250 Alanine, aspartate and glutamate metabolism oke01100 Metabolic pathways oke01232 Nucleotide metabolism oke01240 Biosynthesis of cofactors Module oke_M00049 Adenine ribonucleotide biosynthesis, IMP => ADP,ATP Brite KEGG Orthology (KO)…
Effect of Bootstrapping/Gibbs Sampling in Salmon Counts
Effect of Bootstrapping/Gibbs Sampling in Salmon Counts 2 Hi Everyone, I am a bit confused about the difference between Gibbs Sampling and Bootstrapping when it comes to Salmon and how these procedures affect downstream analysis. For context, I am trying to do analysis of 49 matched cancer vs. normal RNAseq…
Detect contaminating organism
Detect contaminating organism 0 Hello everyone! I am new to bioinformatics and have never faced such a problem, but now I am working with a dataset GSE172189 that appears to be contaminated by bacteria (only ~60% of reads are aligned with Salmon, and taxonomy analysis on SRA says there are…
Comparative transcriptomics between species
Comparative transcriptomics between species 0 Hey all, I am new to the transcriptomics world, therefore I have some questions. I am currently working on a study where the goal is to compare transcriptomes across 5 species. I mapped all rna-seq to reference genomes (different for every species) using Hisat2, then…
TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons
Padeken, J., Methot, S. P. & Gasser, S. M. Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat. Rev. Mol. Cell Biol. 23, 623–640 (2022). Article CAS PubMed PubMed Central Google Scholar Tchasovnikarova, I. A. et al. Epigenetic silencing by the HUSH complex mediates position-effect variegation…
Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics
Albone, E. S. Mammalian semiochemistry. The investigation of chemical signals between mammals. 2–5 (1984). Wyatt, T. D. Pheromones and Animal Behaviour: Communication by Smell and Taste (Cambridge University Press, 2003). Book Google Scholar Doty, R. L. Odor-guided behavior in mammals. Experientia 42, 257–271 (1986). Article CAS PubMed Google Scholar Brennan,…
Phage therapy minimally affects the water microbiota in an Atlantic salmon (Salmo salar) rearing system while still preventing infection
Shreiner, A. B., Kao, J. Y. & Young, V. B. The gut microbiome in health and in disease. Curr. Opin. Gastroenterol. 31, 69–75. doi.org/10.1097/Mog.0000000000000139 (2015). Article CAS PubMed PubMed Central Google Scholar Selber-Hnatiw, S. et al. Human gut microbiota: Toward an ecology of disease. Front. Microbiol. 8, 1265. doi.org/10.3389/fmicb.2017.017E5 (2017)….
Bulk RNAseq Salmon index building which transcriptome to use
Bulk RNAseq Salmon index building which transcriptome to use 0 Hi all, I am new to the platform. I was wondering what the common/best practice is regarding building a Salmon index for bulk RNAseq analysis of human cells. The tutorial for Salmon/Alevin is using the complete transcriptome from GENCODE (gencode.vM23.transcripts.fa.gz,…
Index of /~psgendb/birchhomedir/admin/launchers/biolegato.app/Contents/Resources/pkg/transrate/bin
Name Last modified Size Description Parent Directory – bam-read 2016-06-06 08:37 5.4M libgcc_s.so.1 2019-03-08 21:07 89K libgomp.so.1 2019-03-08 21:07 83K liblzma.so.0 2019-03-08 21:07 132K libm.so.6 2019-03-08 21:07 582K libtbb.so 2019-03-08 21:07 20 libtbb.so.2 2019-03-08 21:07 4.5M libtbbmalloc.so 2019-03-08 21:07 26 …
Pearson correlation for RNAseq data
Pearson correlation for RNAseq data – input formats 0 Hi guys, I work with tiny crustaceans and did RNAseq on different species, each with 3 biological replicates (each replicate being a pool of 3 individuals). I want to check if there is a good correlation between my replicates. I trimmed…
all(rownames(cts) %in% txdf$TXNAME) is FALSE in DTU Analysis in R
Good afternoon, I am trying to do a DTU analysis for my research, but I am kinda new to this stuff and I have some problems. In particular on point 5). I am following the workflow of Bioconductor vignette rnaseqDTU and my pipeline is this: 1) read salmon quants ##…
couldn’t find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function ‘seqinfo’ for signature ‘”SummarizedExperiment”‘
Dear Michael, I have not been able to run tximeta properly. I have read #38 but could not get any clue. The quant.sf files were generated by the latest nf-core RNA-seq pipeline (3.12.0), as the pipeline did not save the Salmon index, I generated it myself. Salmon used by nf-core…
CRISPR Makes History With FDA Approval For Sickle Cell Disease
The U.S. Food and Drug Administration has approved a CRISPR-based treatment for sickle cell disease, an inherited disorder that distorts the shape of red blood cells and disrupts the function of hemoglobin, the protein that carries and distributes oxygen throughout the body. About 1 in 13 Black babies are born…
What methods do you use to quantify protein expression by rna sequencing
RNA sequencing can be used to quantify protein expression using various methods. One approach is to process the RNA sequencing reads using workflows such as Tophat-HTSeq, Tophat-Cufflinks, STAR-HTSeq, Kallisto, and Salmon. These methods have been benchmarked and shown to have high correlations with wet-lab validated qPCR assays for gene expression….
Trinity Insilico Normalization
Trinity Insilico Normalization 1 Hello, I am trying to run trinity but on two samples but I am confused. I need help please. The process tells me this: perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG=”C.UTF-8″ are supported…
Does chromosome order matter when combining individual primary assembly files?
Does chromosome order matter when combining individual primary assembly files? 0 I’m attempting to create a salmon index file for gallus gallus, for which I need both the genome and transcriptome files; from Ensembl, I was able to download the cdna.all transcriptome file as well as the individual chromosome primary…
Solved Now write an R script with the contents shown below
Now write an R script with the contents shown below to import the Salmon alignments into `DESeq2` and perform differential expression analysis. As with the previous script, since I provide the complete script, look up each of the functions used and make sure you understand how they are used here….
Converting STAR Gene-level alignment to TPM expression
Converting STAR Gene-level alignment to TPM expression 0 Hi, I have recently performed gene-level alignment with STAR on 20 samples with the parameter –quantMode GeneCounts and –outSAMtype BAM SortedByCoordinate. I have the output files ReadsPerGene.out.tab and Aligned.sortedByCoord.out.bam. From this, how can I generate reliable TPM values with either the sorted…
Salmon – mapping outputs
Salmon – mapping outputs 0 Hi guys, I am using Salmon for read quantification on my Denovo transcriptomes. Does anyone know how can I get the information on the number (or percentage) of reads that mapped exactly 1 OR more than 1 time (something similar to Bowtie2 output) ? I…
Genomics for monitoring and understanding species responses to global climate change
Smith, T. B. & Bernatchez, L. Evolutionary change in human-altered environments. Mol. Ecol. 17, 1–8 (2008). Article PubMed Google Scholar Bellard, C., Bertelsmeier, C., Leadley, P., Thuiller, W. & Courchamp, F. Impacts of climate change on the future of biodiversity. Ecol. Lett. 15, 365–377 (2012). Article PubMed PubMed Central Google…
Macrophage polarization and metabolism in atherosclerosis
Organization WH the top 10 causes of death. www.who.int/news-room/fact-sheets/detail/the-top-10-causes-of-death, 2019. Rana JS, Khan SS, Lloyd-Jones DM, Sidney S. Changes in mortality in Top 10 causes of death from 2011 to 2018. J Gen Intern Med. 2021;36:2517–8. Article PubMed Google Scholar Libby P. The changing landscape of atherosclerosis. Nature. 2021;592:524–33. Article …
DNA shows where Washington culvert replacemen
image: Co-authors Erin D’Agnese and Maya Garber-Yonts (l-r) sampling upstream of a culvert in Chuckanut Creek in April 2021. The blue backpack contains a pump that sucks stream water through the yellow tubes to filter material for DNA analysis. view more Credit: Elizabeth Andruszkiewicz Allan/University of Washington To help struggling…
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
AnnotationHub data for Mus musculus seems to be missing, while previously it was there 1 @1917db9e Last seen 8 hours ago United States I have been using tximeta to get the annotation data for my RNAseq data, created by salmon. I was previously able to get the annotations for the…
Salmon and SPAdes contigs filtering
Salmon and SPAdes contigs filtering 0 Hello! I have a bunch of reference contigs, obtained with SPAdes, and RNA-seq data analyzed with salmon for control and experimental sample (let it be c_ and 2_). For every gene, there are several contigs, differing by length. Here are some tables Control: ~$…
Bacterial networks in Atlantic salmon with Piscirickettsiosis
Verschuere, L., Rombaut, G., Sorgeloos, P. & Verstraete, W. Probiotic bacteria as biological control agents in aquaculture. Microbiol. Mol. Biol. Rev. 64(4), 655–671 (2000). Article CAS PubMed PubMed Central Google Scholar Gomez, G. D. & Balczar, J. L. A review on the interactions between gut microbiota and innate immunity of…
conda – How to install Bioconda packages
The Bioconda channel builds packages with the Conda Forge channel prioritized. This requires users to likewise prioritize the Conda Forge channel when installing Bioconda packages (see Bioconda documentation). That is, the correct formulation for specifying channels at install time is: conda install -c conda-forge -c bioconda foo Global configuration and…
Genome-wide chromatin interaction map for Trypanosoma cruzi
Johnson, P. J., Kooter, J. M. & Borst, P. Inactivation of transcription by UV irradiation of T. brucei provides evidence for a multicistronic transcription unit including a VSG gene. Cell 51, 273–281 (1987). Article CAS PubMed Google Scholar Matthews, K. R., Tschudi, C. & Ullu, E. A common pyrimidine-rich motif…
Issues with Mixture file when using CIBERSORTx
Hi, I am trying to run a deconvolution analysis of bulk-RNAseq samples using the LM22 signature matrix provided. I converted all ENSEMBL ID’s to their Symbol, and removed NA and duplicated entries. counts_salmon <- as.data.frame(txi$counts) counts_salmon$symbol <- mapIds(org.Hs.eg.db, keys = rownames(counts_salmon), column = “SYMBOL”, keytype = “ENSEMBL”) counts_salmon <- counts_salmon…
Salmon loop on multiple samples
Salmon loop on multiple samples 0 Hi everyone! I’m entering the bioinformatics world, and I have some problems with Salmon. In particular, I have to perform salmon on 101 pair-end samples (no replicates). I could do it one by one, but I think it is prone to errors. I tried…
ISOTHERMAL RECOMBINANT POLYMERASE AMPLIFICATION AND CRIPSR(CAS12A) ASSAY DETECTION OF RENIBACTERIUM SALMONINARUM AS AN EXAMPLE FOR WILDLIFE PATHOGEN DETECTION IN ENVIRONMENTAL DNA SAMPLES
doi: 10.7589/JWD-D-22-00128. Online ahead of print. Affiliations Expand Affiliations 1 University of Washington, School of Marine and Environmental Affairs, 3737 Brooklyn Ave. NE, Seattle, Washington 98105, USA. 2 Wild EcoHealth LLC, Tacoma, Washington 98465, USA. 3 U.S. Geological Survey, Western Fisheries Research Center, 6505 Northeast 65th St., Seattle, Washington 98115,…
tximport error: vroom
when i trying import a list of salmon counts files quant.sf: txi <- tximport(files=files, type=”salmon”, tx2gene=tx2gene[,c(“refseq”, “entrezid”)], countsFromAbundance=”lengthScaledTPM”) Rstudio throw me a error: reading in files with read_tsv 1 Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, : bad value why did it happen? Here are files…
rna-seq analysis with Salmon – how to Import and summarize using tximport
Hi! I’m trying to do RNA-seq analysis using salmon and would like to have a matrix of read counts of 10 RNA fastq files. I installed salmon with bioconda, however, I can only find version : 0.8.1 even after ‘conda update salmon’. So I have been doing with version 0.8.1…
TPM from STAR output without re-allign the file using RSEM or Salmon
Hi, I want to get the TPM files from aligned files generate with STAR and reading I found out that the easiest way is using RSEM or Salmon. My code for the alignment is /Users/c/STAR/bin/MacOSX_x86_64/STAR runThreadN 4 –genomeDir /Users/c/Desktop/Human_genome_index –readFilesIn /Users/c/Desktop/test/C1D20_R1_001_paired.fastq /Users/c/Desktop/test/C1D20_R2_001_paired.fastq –quantMode TranscriptomeSAM GeneCounts –outFileNamePrefix C1D20 –outSAMtype BAM SortedByCoordinate…
Comparing multiple RNASeq studies
Comparing multiple RNASeq studies 0 I am looking to perform a cumulative analysis of data from multiple RNASeq studies deposited online. Some of the studies uploaded the raw fastq files, but others only upload a post raw mapping counts table or normalized counts ex) zenodo.org/record/4114617 I do not have the…
Aquaculture Vaccine Market Poised to reach US$ 913.6 Million by 2033, Fuelled by Rising Global Aquaculture Production: FMI Study
The global Aquaculture Vaccines Market is worth US$ 406 Million as of now and is expected to reach US$ 913.6 Million by the year 2033 at a CAGR of 8.5% between 2023 and 2033. Surge in aquaculture is the factor majorly driving the aquaculture vaccines market. There is an ever-increasing…
Salmon alignment based quantification
Salmon alignment based quantification 1 Hi, I aligned my sequences with STAR alignment and I need to quantify them with salmon with alignment based quantification mode. So I wonder > ./bin/salmon quant -t transcripts.fa -l <LIBTYPE> -a aln.bam -o salmon_quant In the command above, what should I write to transcripts.fa…
High amount of intronic/intergenic reads in SMARTer stranded total bulk RNAseq
High amount of intronic/intergenic reads in SMARTer stranded total bulk RNAseq 0 Hello, I have bulk RNAseq data (SMARTer, stranded total RNA with ribo depletion, 100M paired-end reads 150bp) of 12 human samples and the QC stats look like this High mapping rate against the genome (~90% with Hisat2/STAR) Low…
How to check RNAseq support for annotated genes?
How to check RNAseq support for annotated genes? 2 Hello All, I have a set of annotated genes in gff3 format and corresponding RNA-seq data. What is the recommended approach and are there specific tools and parameters to determine the percentage of genes supported by the RNA-seq data?” Regards, B…
Salmon index not progressing
Salmon index not progressing 0 Hi! I am having issue with salmon index formation since I cannot use STAR due to limited amount of RAM (as per my recent post). I tried to follow this tutorial on how to create decoy-aware transcriptome as well as doing directly this and I…
The Power of Metagenomics – Fish Farmer Magazine
State-of-the art DNA surveillance can surpass current diagnostics approaches Aquaculture is under pressure. Last year’s Salmon Production Survey revealed that even though output marginally increased in 2021, the general trend of decreasing Year 2 survival continues. This alarming drop in fish health also results in economic loss. Mortalities arise when…
Refseq annotation | Populus trichocarpa
Refseq annotation | Populus trichocarpa 0 Hello, I would like to annotate a salmon output dataset with the RefSeq accession numbers (i.e NM_001404768.1, XM_002297615.4). I keep coming across this way of doing it using org.Hs.eg.db, but it’s not working with RefSeq and mostly plant organisms (as I work on Populus…
Somatic SLC30A1 mutations altering zinc transporter ZnT1 cause aldosterone-producing adenomas and primary aldosteronism
Young, W. F. Primary aldosteronism: renaissance of a syndrome. Clin. Endocrinol. 66, 607–618 (2007). Article CAS Google Scholar Rossi, G. P. et al. A prospective study of the prevalence of primary aldosteronism in 1,125 hypertensive patients. J. Am. Coll. Cardiol. 48, 2293–2300 (2006). Article CAS PubMed Google Scholar Fardella, C….
Genetically Modified Organism (GMO)
Genetically Modified Organism (GMO) What is Genetically Modified Organism (GMO)? About: A genetically modified organism (GMO) refers to an entity, whether it’s an animal, plant, or microorganism, that has undergone modifications to its DNA using genetic engineering methods. Across generations, specific traits have been cultivated in crops…
A comprehensive genomic catalog from global cold seeps
Joye, S. B. The geology and biogeochemistry of hydrocarbon seeps. Annu. Rev. Earth Pl. Sci. 48, 205–231 (2020). Article ADS CAS Google Scholar Al-Shayeb, B. et al. Borgs are giant genetic elements with potential to expand metabolic capacity. Nature 610, 731–736 (2022). Article ADS CAS PubMed PubMed Central Google Scholar …
Analysis of cnidarian Gcm suggests a neuronal origin of glial EAAT1 function
Araque, A. & Navarrete, M. Glial cells in neuronal network function. Philos. Trans. R. Soc. Lond. B Biol. Sci. 365, 2375–2381 (2010). Article PubMed PubMed Central Google Scholar Verkhratsky, A. & Butt, A. Glial Physiology and Pathophysiology 73–104 (John Wiley & Sons Ltd, 2013). Google Scholar Zhang, Y. & Barres,…
Multiplexed transcriptomic profiling of the fate of human CAR T cells in vivo via genetic barcoding with shielded small nucleotides
Wagner, A., Regev, A. & Yosef, N. Revealing the vectors of cellular identity with single-cell genomics. Nat. Biotechnol. 34, 1145–1160 (2016). Article CAS PubMed PubMed Central Google Scholar Gehring, J., Hwee Park, J., Chen, S., Thomson, M. & Pachter, L. Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular…
How to properly compare the group-specific samples using DEseq2
I am trying to analyze the RNAseq data using Salmon + DEseq2. I have two variables: genotype (WT or KO) + condition ( treatment A or B), as shown below: >samples # run genotype condition #sample1 sample0001_quant WT A #sample2 sample0002_quant WT B #sample3 sample0003_quant KO A #sample4 sample0004_quant KO…
Differential Expression using Isoseq-supplemented reference transcriptome
Differential Expression using Isoseq-supplemented reference transcriptome 1 Hi all, I have a dataset of Illumina short read RNA-Seq data from (n = 6 per group) three different mouse genotypes, and paired PacBio Isoseq data from a subset of these (n = 2 per group). I have processed the IsoSeq data…
We’re All Suspects in a DNA Lineup, Waiting to Be Matched With a Crime
John Whitehead “Make no mistake about it…your DNA can be taken and entered into a national DNA database if you are ever arrested, rightly or wrongly, and for whatever reason… I doubt that the proud men who wrote the charter of our liberties would have been so eager to…
What to do after importing quantification with tximport
What to do after importing quantification with tximport 1 I am doing the classic pipeline for DGE Analysis. I have quantified some rna-sequences with Salmon and now I have imported them with tximport package (as the vignette says). I am new to the field and I am stuck at this…
RefSeq: XP_013985108
LOCUS XP_013985108 229 aa linear VRT 07-JAN-2022 DEFINITION esterase OVCA2 isoform X1 [Salmo salar]. ACCESSION XP_013985108 VERSION XP_013985108.1 DBLINK BioProject: PRJNA788898 DBSOURCE REFSEQ: accession XM_014129633.2 KEYWORDS RefSeq. SOURCE Salmo salar (Atlantic salmon) ORGANISM Salmo salar Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmoninae; Salmo. COMMENT…
Colossal Biosciences “Mammoth in the Classroom” Initiative, as Part of University of Alaska Fairbanks Adopt a Mammoth Program, Has Reached Its Initial Research and Adoption Goal | News
DALLAS–(BUSINESS WIRE)–Aug 21, 2023– In the largest initiative of American mammoth research ever conducted, Colossal Biosciences, the breakthrough genetic engineering and de-extinction company, in partnership with the University of Alaska Fairbanks, has announced that the first-of-its-kind “Mammoth in the Classroom” initiative has reached its initial research and adoption goal. Through…
Creating tx2gene table from sheep transcripts IDs to gene IDs using NCBI annotation file
Creating tx2gene table from sheep transcripts IDs to gene IDs using NCBI annotation file 0 Hello, I am trying to create a tx2gene table using NCBI annotation file (GCF_016772045.1) ramb_gtf <- import(“genomic.gtf”) txdb <- makeTxDbFromGRanges(ramb_gtf) k <- keys(txdb, keytype = “GENEID”) df <- select(txdb, keys = k, columns = “TXNAME”,…
How to combine only reads columns from 6 different NM transcript ID based quant.sf files
How to combine only reads columns from 6 different NM transcript ID based quant.sf files 1 Hello, Being beginner, I want to just know what is the simplest way to combine only read columns from 6 different NM transcript based quant.sf files. These transcript belongs to sheep and I want…
Pathological analysis and antimicrobial susceptibility of Chryseobacterium balustinum RTFCP 298 isolated from diseased rainbow trout, Oncorhynchus mykiss
Vandamme, P., Bernardet, J. F., Segers, P., Kersters, K. & Holmes, B. New perspectives in the classification of the Flavobacteria: Description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. Rev. Int. J. Syst. Bacterial. 44, 827–831 (1994). Article Google Scholar Bernardet, J. F., Nakagawa, Y. & Holmes, B….
Open data to power up blue economy
EMBL-EBI Senior Scientist Rob Finn explains why data coordination and sharing are fundamental for a sustainable blue economy Rob Finn, EMBL Senior Scientist and Head of Microbiome Informatics at EMBL-EBI. Photo credit: Jeff Dowling/EMBL-EBI For the life sciences to make major contributions to the blue economy, data needs to be…
Snohomish County receives $9.9 million grant for Snohomish River Basin
SNOHOMISH COUNTY, Wash., August 9, 2023 – Snohomish County’s Community Floodplain Solutions (CFS) program has received a third grant of $9.9 million from the Washington State Department of Ecology’s Floodplains by Design (FbD) program. CFS Phase 3 is the continuation of integrated floodplain management work that was funded by two…
Sample number dependent unigene increase with De Novo assembly
Sample number dependent unigene increase with De Novo assembly 0 I am analyzing eukaryotic RNA-seq results using the De Novo assembly. I initially analyzed the sequencing reads from four samples of the same eukaryote species, and later added two samples of the same species (n=6 in total). As a result,…
About rnaseq_salmon
RNAseq Salmon (rnaseq_salmon) is a DNAnexus Workflow that combines the two DNAnexus applets Salmon Scatter-Process-Gather Workflow and quant_sf2express_table. Salmon Scatter-Process-Gather Workflow (salmon_spg_wf) is a DNAnexus applet that process a batch of pair-end FASTQ read files and runs Salmon to produce expression count files. quant_sf2express_table is a DNAnexus applet that generates expression table files suitable for RNA-seq Expression…
Bulk RNASeq: from counts to differential expression
This course consists of a live session on counting and differential expression analysis in R and a Q&A session to answer all the questions that arise when trying the analysis on your own data. The live session will demonstrate R tools to generate count files like featureCounts, and summarizeOverlaps are…
The meaning of wild: Genetic and adaptive consequences from large-scale releases of domestic mallards
Grabenstein, K. C. & Taylor, S. A. Breaking barriers: causes, consequences, and experimental utility of human-mediated hybridization. Trends Ecol. Evol. 33, 198–212 (2018). Article PubMed Google Scholar Crispo, E., Moore, J. S., Lee‐Yaw, J. A., Gray, S. M. & Haller, B. C. Broken barriers: human‐induced changes to gene flow and…
Mapping global biodiversity in Finland
Oulanka National Park’s unique river system is rich in rare flora and fauna. Image: RawPixel/Shutterstock Bryony Cottam joins an expedition collecting environmental DNA in Finland as part of an ambitious plan to map global biodiversity Do you know what to do if you meet a bear in the woods?’ Martti…
Invasion success of a Lessepsian symbiont-bearing foraminifera linked to high dispersal ability, preadaptation and suppression of sexual reproduction
Simberloff, D. et al. Impacts of biological invasions: What’s what and the way forward. Trends Ecol. Evol. 28, 58–66 (2013). Article PubMed Google Scholar Bellard, C., Cassey, P. & Blackburn, T. M. Alien species as a driver of recent extinctions. Biol. Lett. doi.org/10.1098/rsbl.2015.0623 (2016). Article PubMed PubMed Central Google Scholar …
Salmon error (ex. transcript id appears in the BAM head, but was not in the provided FASTA file)
Salmon error (ex. transcript id appears in the BAM head, but was not in the provided FASTA file) 1 Hello. everyone I am trying to count aligned reads using Salmon in alignment-based mode. My command is: salmon quant -t transcript.fa -l A -a aligned_result.bam -o salmon_quant I am encountering the…
GTF file tomato
GTF file tomato 1 HI Everybody I’d like to run the mapping of tomato reads; But not able to find the GTF file. Is there a way to locate this format or convert the GFF file into GTF. tomato GTF GFF • 40 views Visit : www.ncbi.nlm.nih.gov/datasets/taxonomy/4081/ Click on Download…
transcripts missing from tx2gene
transcripts missing from tx2gene 2 How can I know the reference trascriptome used in the pre-computed index ? You can download the fasta transcriptome file archive (fasta, .fai index and chrome.sizes) used for that index here: refgenomes.databio.org/v3/assets/archive/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/fasta_txome?tag=default This should get you the table you need $ grep “^>E” 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4.fa |…
Infocusp Innovations hiring Senior Bioinformatics Scientist in Pune, Maharashtra, India
Infocusp Innovations is an IT firm working in the broad fields of Machine Learning, Artificial Intelligence (AI), Computer Science, Software Engineering, Mobile and Web App Development, QA, and Signal Processing. Headquartered in Ahmedabad and having a branch office in Pune, we make businesses smart and systems smarter to make people’s…
Randomizing reads for Salmon
Randomizing reads for Salmon 0 Hi Biostars community, I want to run Salmon with aligned samples. I only have sorted BAMs, and the way Salmon works, it needs the reads to be randomized in the input file. Will sorting by read name effectively shuffle the reads? I have paired-end data,…
Salmon_index.json doesn’t seem to exist
Good evening, thanks to a previous post I was able to solve one problem in my pipeline. Now I am dealing with another one. I have to quantify some rna sequence with salmon and I downloaded a pre-computed index from the link suggested in salmon documentation. The link is this,…
Extensive pedigrees reveal the social organization of a Neolithic community
Fox, R. Kinship and Marriage: An Anthropological Perspective (Cambridge Univ. Press, 1983). Morgan, L. H. Ancient Society: Or, Researches in the Lines of Human progress from Savagery, Through Barbarism to Civilization (C. H. Kerr, 1877). Lévi-Strauss, C. The Elementary Structures of Kinship (Beacon Press, 1971). Schneider, D. M. A Critique…
DEseq2 input from nf-core/rnaseq
DEseq2 input from nf-core/rnaseq 1 I used the nf-core/rnaseq pipeline in the cluster human genome, and I got some files as the output of Star salmon. My question is which file I use as input to DESeq2? and where is the full file that contains 58,000 genes? salmon.merged.gene_counts_length.tsv (29744 genes)…
Adding Salmon Alevin counts to clustered Seurat object
Adding Salmon Alevin counts to clustered Seurat object 0 Hi Im trying to figure out an appropriate way to add Salmon Alevin count matrix to a previously created and clustered Seurat object, just to be able to see isoform distribution across clusters generated from scRNA-seq data. I can import Alevin…
Desq2 input from nf-core/rnaseq
Desq2 input from nf-core/rnaseq 0 I used the nf-core/rnaseq pipeline in the cluster human genome, and I got some files as the output of Star salmon. My question is which file I use as input to DESeq2? and where is the full file that contains 58,000 genes? salmon.merged.gene_counts_length.tsv (29744 genes)…
Problem creating salmon index
Problem creating salmon index 1 Good evening, I need to align some rna sequences from some data with salmon. I am trying to create an index with salmon using this command: salmon index -t GRCh38_latest_rna.fna.gz –index tindex where the zipped file is downloaded from this link: www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml selecting the transcriptome…
DMF, H-151 treatments may help target autoimmune inflammation in ALS | Cell study proposes DMF, H-151 for clinical testing in sporadic ALS
Dimethyl fumarate (DMF) — an oral medication approved for multiple sclerosis — and H-151, an experimental treatment, can suppress inflammatory and abnormal immune pathways thought to be involved in sporadic amyotrophic lateral sclerosis (ALS). These are the findings of a study using immune cells from sporadic ALS patients that also…
Rise in Consumption of Salmon and Tilapia to drive the Aquaculture Vaccines Market, reaching US$ 913.6 Million by the year 2033 a CAGR of 8.5%
The global Aquaculture Vaccines Market is worth US$ 406 Million as of now and is expected to reach US$ 913.6 Million by the year 2033 at a CAGR of 8.5% between 2023 and 2033. Surge in aquaculture is the factor majorly driving the aquaculture vaccines market. There is an ever-increasing…
are not unique. in Build Transcript and Gene Expression Matrices
How to solve, Error, the column headings: are not unique. in Build Transcript and Gene Expression Matrices 0 I’m trying to generate Build Transcript and Gene Expression Matrices, my command is: /trinityrnaseq-v2.13.2/util/abundance_estimates_to_matrix.pl –est_method salmon Sy_Externa_1/quant.sf Sy_Externa_2/quant.sf Sy_Externa_3/quant.sf Sy_Externa_4/quant.sf Sy_Externa_5/quant.sf Sy_Externa_6/quant.sf Sy_Externa_7/quant.sf Sy_Interna_1/quant.sf Sy_Interna_2/quant.sf Sy_Externa_3/quant.sf Sy_Externa_4/quant.sf –gene_trans_map none –name_sample_by_basedir * Outputting…
The Report provides complete market analysis of Biotechnology market and reports related to this market, forecasted for period from 2023
PRESS RELEASE Published July 10, 2023 Biotechnology Market The Biotechnology market was valued at 528940 million in 2023 and is projected to reach US$ 856060 million by 2030, at a CAGR of 7.1% during the forecast for period from 2023 – 2030. The biotechnology market research report provides insights into…
Quantify Isoforms in RNA-Seq data
Quantify Isoforms in RNA-Seq data 2 Hi everyone, I know this question has been asked multiple times in other posts, but I am still not clear. I want to quantify counts for each isoforms. I am not sure how it will be possible specially for overlapping transcripts. I think featurecounts…
Staff Bioinformatics Scientist – San Leandro
Bioinformatics Scientist We are seeking a highly motivated and skilled Bioinformatics Scientist to join our R&D team. The successful candidate will be integral to our genomics research efforts. This role requires expertise building pipelines from sequencer output to feature generation from both RNA and DNA sources. The candidate should have…