Tag: Salmon

Yang, Q. L., Gao, T. X. & Miao, Z. Q. Differentiation between populations of Japanese grenadier anchovy (Coilia nasus) in Northwestern Pacific based on ISSR markers: Implications for biogeography. Biochem Syst and Ecol 39, 286–296 (2011). CAS  Google Scholar  Shen, H. S. et al. In-depth transcriptome analysis of Coilia ectenes,…

Makhalanyane TP, Valverde A, Gunnigle E, Frossard A, Ramond JB, Cowan DA. Microbial ecology of hot desert edaphic systems. FEMS Microbiol Rev. 2015;39:203–21. Article  CAS  PubMed  Google Scholar  Pointing SB, Belnap J. Microbial colonization and controls in dryland systems. Nat Rev Microbiol. 2012;10:551–62. Article  CAS  PubMed  Google Scholar  Ji M,…

Docker Error while running nf-core/rnaseq pipeline 1 I have run a nf-core pipeline with the following parameters: nextflow run nf-core/rnaseq -r 3.10.1 –input samplesheet.csv –outdir outputlatest –fasta chr22_with_ERCC92.fa -profile docker –gtf chr22_with_ERCC92.gtf –skip_multiqc true –skip_dupradar true –skip_stringtie true –aligner star_salmon –pseudo_aligner salmon –max_memory 3.5GB –max_cpus 4 Receiving an error related…

NLRP3 expression and purification Both wild-type NLRP3 and CAPS mutants were cloned in the mammalian expression vector pcDNA3.1HisB. Plasmid was purified using Qiagen Giga Prep up to 2000 ng/μl and subsequently transfected into Expi293 with Expifectamine per manufacturer instructions. Expression was allowed to proceed for 3 days before harvesting. Cells were…

Salmon Index 1 Hello, I had a question about indexing with Salmon. I saw on the Salmon github pipeline that you can use the cDNA sequence with no alterations to create the index. curl ftp.ensemblgenomes.org/pub/plants/release-28/fasta/arabidopsis_thaliana/cdna/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa.gz -o athal.fa.gzenter salmon index -t athal.fa.gz -i athal_index But on Salmons documentation they say there…

Entry EC 4.2.1.141                Enzyme                                  Name 2-dehydro-3-deoxy-D-arabinonate dehydratase Class Lyases;Carbon-oxygen lyases;Hydro-lyasesBRITE hierarchy Sysname 2-dehydro-3-deoxy-D-arabinonate hydro-lyase (2,5-dioxopentanoate-forming) Reaction(IUBMB) 2-dehydro-3-deoxy-D-arabinonate = 2,5-dioxopentanoate + H2O [RN:R09186] Reaction(KEGG) Substrate 2-dehydro-3-deoxy-D-arabinonate [CPD:C03826] Product Comment The enzyme participates in pentose oxidation pathways that convert pentose sugars to the tricarboxylic acid cycle intermediate 2-oxoglutarate. History EC 4.2.1.141 created 2013 Pathway…

Transcript Directionality with Unstranded Single End Reads ? 1 I am working with Single End cDNA transcriptomic data and it has been determined by Salmon using the auto detect method evoked by the -l A or –libType A options that the raw reads are unstranded. My question is whether or…

Different read numbers for the same samples 1 I have 5 groups of interest for my rnaseq, where I also broke it down into a 3 group version for simplicity. What I am confused by is when I look at the single gene reads for the same groups in different…

Mandáková, T. & Lysak, M. A. Post-polyploid diploidization and diversification through dysploid changes. Curr. Opin. Plant Biol. 42, 55–65 (2018). Article  PubMed  Google Scholar  Blanc, G. & Wolfe, K. H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16, 1667–1678 (2004). Article  CAS …

Bol’shakov, S.G., Some features of biology, growth, and age of Far Eastern redfins—Pacific redfin Tribolodon brandti and big-scaled redfin Tribolodon hakonensis—in southern Primorskii krai, Izv. Tikhookean. Nauchno-Issled. Inst. Rybn. Khoz. Okeanogr., 2013, pp. 141–158. Google Scholar  Brykov, V.A., Polyakova, N.E., and Semina, A.V., Comparative analysis of mitochondrial DNA variability in four…

Elmore, S. Apoptosis: A review of programmed cell death. Toxicol. Pathol. 35, 495–516 (2007). Article  CAS  PubMed  PubMed Central  Google Scholar  Shi, Y. Caspase activation, inhibition, and reactivation: A mechanistic view. Protein Sci. 13, 1979–1987 (2004). Article  CAS  PubMed  PubMed Central  Google Scholar  Alberts, B., Johnson, A. & Lewis, J….

Metatranscriptomics de novo assembly pipeline how to annotate/quantify 0 Hello, I am new to metatranscriptomics and would like some advice on processing raw reads from a metatranscriptomics project. I am looking at soil samples under various treatment conditions and therefore would like to do a de novo assembly approach. I…

In today’s world, there is an increased emphasis on eating healthy and being environmentally friendly. One of the key factors in achieving these goals is the source of the food we eat. Consumers are now more conscious of where their food comes from and want to be sure that it…

Anderson MJ (2001) A new method for non‐parametric multivariate analysis of variance. Austral Ecol 26(1):32–46 Google Scholar  Anderson MJ (2004) PERMDISP: a FORTRAN computer program for permutational analysis of multivariate dispersions (for any two-factor ANOVA design) using permutation tests. Department of Statistics, University of Auckland, New Zealand, 24. Aykanat T,…

Salmon for RNAseq alignement? 0 Hi everyone! I’m new in this world of transcriptomics and need some help. I have the .fastq files from an RNAseq experiment, there are filtered through fastp in default settings. Someone suggested that I can use Salmon to align my .fastq files to the reference…

(The Conversation is an independent and nonprofit source of news, analysis and commentary from academic experts.) (THE CONVERSATION) Ocean life is largely hidden from view. Monitoring what lives where is costly – typically requiring big boats, big nets, skilled personnel and plenty of time. An emerging technology using what’s called…

Historical Background  The WSU College of Agricultural, Human and Natural Resource Sciences (CAHNRS) traces its origins to our Land-grant University’s founding. Only five months after attaining statehood, the Washington State Legislature established the Washington State Agricultural College, Experiment Station and School of Sciences on March 28, 1890. Instruction began in…

Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq? 1 Or “Everything You Always Wanted to Know About RNA-Seq (But Were Afraid to Ask) Part 2” In RNA-Seq, it is common practice to compare the abundance of transcripts within the same sample after some form of…

scaledTPM for DESeq2 using tximport 1 @ffcc7fa5 Last seen 3 hours ago India Hello! I am performing a transcript level differential expression analysis. For the same, I have quantified my samples using salmon and am using tximport as an offset before DESeq2. I wanted to know whether passing scaledTPM values…

What is the best aligner for stranded RNASeq 2 If you only need to quantify expression at the transcript/gene level, use Salmon or Kallisto. If you need to align reads to the transcriptome or genome go with STAR. Not sure about the best aligner, but there are some aligners that…

How does salmon uses polyester? 1 Hi Salmon users or developers! In salmon paper, to evaluate the ground truth, it uses RSEM to a certain data and uses polyester to the output of RSEM. Why use polyester on the output of RSEM? In salmon github repo, can somebody direct me…

Allis CD, Jenuwein T. The molecular hallmarks of epigenetic control. Nat Rev Genet. 2016;17:487–500. Article  CAS  PubMed  Google Scholar  Boccaletto P, Stefaniak F, Ray A, Cappannini A, Mukherjee S, Purta E, et al. MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic Acids Res. 2022;50:D231–D235. Article  CAS  PubMed  Google…

Researchers at the Norwegian University of Science and Technology (NTNU) have been able to keep salmon fry bacteria free for as long as 12 weeks after they have hatched. Credit: Alexander Fiedler, NTNU In the last 10 years, the accessibility and affordability of next generation sequencing has revolutionized research. Forensic…

PRESS RELEASE Published April 26, 2023 Towel Market Size is projected to Reach Multimillion USD by 2029, In comparison to 2022, at unexpected CAGR during the forecast Period 2023-2029. Updated Report with [122] pages. The Readers in the section will understand how the Towel market scenario changed across the globe…

tx2gene.txt : transcript-to-gene mapping file 0 Hi, I am trying to quantify gene count from transcript abundance (from kallisto, salmon etc.) using Tximport. For that i have to create a transcript to gene mapping file. How can i create this? I created one with from GCF_013265735.2_USDA_OmykA_1.1_rna.fasta (Rainbow trout) fro ncbi…

The technology Digital PCR technologies are a greatly improved version of conventional PCR (Fig. 1), allowing absolute quantification of target nucleic acids in a sample. The preparation of the reaction setup bears much resemblance to other commonly used types of PCR. However, unlike quantitative real-time PCR (qPCR), for example, where amplicon…

Lom J, Dyková I. Myxozoan genera: definition and notes on taxonomy, life-cycle terminology and pathogenic species. Folia Parasitol. 2006;53:1–36. Article  Google Scholar  Køie M. Parvicapsula spinachiae n. sp. (Myxozoa, Parvicapsulidae) in Spinachia spinachia (L.) (Teleostei, Gasterosteidae) from Denmark. Parasitol Res. 2003;90:445–8. Article  PubMed  Google Scholar  Jones S, Prosperi-Porta G, Dawe…

Read counting in RSEM and Salmon (alignment mode) 1 Hi all, I was wondering if someone can clarify an issue for me. When counting reads for RNA-seq, you can use EM-based algorithms to correctly assign multimapping reads. Thus, if you have 5 single-end reads that map to 1 transcript, and…

Ma, Y. et al. Gut microbiota adaptation to high altitude in indigenous animals. Biochem. Biophys. Res. Commun. 516, 120–126 (2019). Article  CAS  PubMed  Google Scholar  Guo, N. et al. Seasonal dynamics of diet-gut microbiota interaction in adaptation of yaks to life at high altitude. NPJ Biofilms Microbiomes 7, 38 (2021)….

Ethics statement All experiments were conducted in accordance with the Declaration of Helsinki and the study was approved by the University of Chicago Institutional Review Board, IRB 22-0707. For model training, patients were included from the TCGA breast cancer cohort (BRCA)26. For validation, anonymized archival tissue samples were retrieved from…

New York, April 13, 2023 (GLOBE NEWSWIRE) — The Commercial Aquaculture Vaccines Market is estimated to generate US$ 265.0 million in revenue globally for 2022 and reach a CAGR of 7.9% to attain a valuation of over US$ 605.5 million by the end of 2033. The increasing demand for seafood,…

Cells Human cervix epitheloid carcinoma HeLa cells (ECACC 93021013; RRID:CVCL_0030) were cultured at 37 °C in Dulbecco′s Modified Eagle′s Medium (DMEM) with 3 mM glutamine, 10% (v/v) fetal calf serum (FCS), 10 mM HEPES, 100 IU/ml penicillin, 100 μg/ml streptomycin, and 5 mM glucose in humidified air with 5% CO2. Human osteosarcoma 143B cells were purchased…

Anantharaman V, Koonin EV, Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res. 2002;30:1427–64. doi.org/10.1093/nar/30.7.1427. Article  CAS  PubMed  PubMed Central  Google Scholar  Fernández-Moya SM, Estévez AM. Posttranscriptional control and the role of RNA-binding proteins in gene regulation in trypanosomatid protozoan parasites. Wiley Interdiscip Rev…

Joye, S. B. The geology and biogeochemistry of hydrocarbon seeps. Annu. Rev. Earth Planet. Sci. 48, 205–231 (2020). Article  CAS  Google Scholar  Feng, D. et al. Cold seep systems in the South China Sea: An overview. J. Asian Earth SCI 168, 3–16 (2018). Article  Google Scholar  Dubilier, N., Bergin, C….

Nextflow rnaseq finishing early 0 Hi I’m running the RNA-seq pipeline from nextflow and I have been running it without problems until this dataset it just stops prematurely saying it has finished when it doesn’t even aligns the reads with salmon. Any ideas what may be going on? I have…

Anti-Epithelial cell adhesion molecule (EpCAM) Aptamer(Cat#: CTApt-100) This product is an aptamer which binds to the Cancer stem cell marker epithelial cell adhesion molecule with an affinity of 54.5 nM . Specifications Target Category Protein Target Cancer stem cell marker…

Fig. 6. Characterization of pathogenic and non-pathogenic SLE-derived monoclonal antibodies categorized as anti-dsDNA. a Ig… Fig. 6. Characterization of pathogenic and non-pathogenic SLE-derived monoclonal antibodies categorized as anti-dsDNA. a Ig gene usage, mutation number and CDR3 amino acid sequences of monoclonal antibodies 32.B9, 33.H11, 33.C9, and RH-14. b–d Mutated and…

BULK mRNA-seq with UMIs. Does it make sense to run bedtools genomecov? 0 Hi, I am using BULK rna-seq which includes UMI added after cDNA fragmentation, before PCR amplification (see my previous post BULK mRNA-seq with UMIs. Do I need to normalize by gene length? ). I am trying to…

Can I use abundance from Tximport to compare the expression level of transcript in same condition? 0 I wanted to compare different transcript of the same gene to get an idea which one is expressed more than other. For this I have 3 samples. I did the alignment using Salmon…

Fastqc lsequence duplication and per base sequence content failed 1 I have around 150bp, paired-end RNA-seq data of 321 samples with around 30 Million reads per sample and I am interested in quantifying the expression for the transcriptome-wide association studies (TWAS). I have performed QC using fastqc. The per base…

Credit: Unsplash/CC0 Public Domain The small size and isolation of the endangered population of Southern Resident killer whales in the Pacific Northwest have led to high levels of inbreeding. This inbreeding has contributed to their decline, which has continued as surrounding killer whale populations expand, according to research published in…

The small size and isolation of the endangered population of Southern Resident killer whales in the Pacific Northwest have led to high levels of inbreeding. This inbreeding has contributed to their decline, which has continued as surrounding killer whale populations expand, according to research published in Nature Ecology and Evolution….

How to quantify the expression of CD45 isoforms from bulk RNA-seq data 0 I used Salmon to quantify transcripts from bulk RNA-seq data and generated gene-level quantifications with the summarizeToGene function from the taximeta package. Now I’m interested in quantifying the expression of specific CD45 isoforms, such as CD45RA and…

Converting an output de-novo transcriptome assembled with Trinity to a .gff3 file 2 Hello! I’ve de-novo assembled a transcriptome from Trinity, resulting into Trinity.fasta, whose headers look like this: >TRINITY_DN29256_c0_g1_i1 len=323 path=[0:0-322] Followed, in the next line, by the sequence. To run an external downstream analysis with a R script,…

Avgerinos GC, Drapeau D, Socolow JS, Mao J, Hsiao K and Broeze RJ (1990) Spin filter perfusion system for high density cell culture: production of recombinant urinary type plasminogen activator in CHO cells. Bio/Technology 8: 54–58. Article  CAS  Google Scholar  Bichay JT, Adams EG, Inch RW, Brewer JE and Bhuyan…

Hi, I am attempting to work through the workflow described in “Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.” I am running into an error message when I try to make the counts dataframe for DRIMseq: Error in data.frame(gene_id = txdf$GENEID, feature_id = txdf$TXNAME, cts) : arguments…

Standard Differentiation between a pathogenic and a non-pathogenic form of Gyrodactylus salaris using PCR-RFLP. / Kania, Per Walther; Jørgensen, Thomas Rohde; Buchmann, Kurt. In: Journal of Fish Diseases, Vol. 30, No. 2, 2007, p. 123-126. Research output: Contribution to journal › Journal article › peer-review Harvard Kania, PW, Jørgensen, TR…

Big BCV (Biological Coefficient of Variation) – no sense to continue the analysis of differential gene expression? 2 Is it possible to perform differential gene expression analysis on data with such dispersion, BCV and MDSplot? (Fig. A, B) y_disp_design <- estimateDisp(y_filtered, design = design) y_disp_design$common.dispersion 0.3251901 Is it possible to…

Animals All the procedures and protocols were approved by the Institutional Animal Care and Use Committee of the National Institute for Basic Biology (15A005, 14A003, 13A023, 12A020, 11A028) and Kyushu University (A21-043-0, A19-137-0, A19-137-1, A19-137-2, A29-088-0, A29-088-1, A29-088-2). Japanese medaka (Oryzias latipes) were bred and maintained under artificial reproductive conditions…

I am working on analysis for an RNASeq experiment with the end goal of using DESeq2 to generate a list of differentially expressed genes. We have 4 biological replicates for 4 conditions (differing genotypes in mice). We have 50 bp single ended Illumina read sets, on total RNA (they had…

Forum:How does CIBERSORTx deal with multiple HGNC symbol rows 0 After obtaining my counts matrix from salmon and assigning HGNC symbols to my ENGS IDs, I end up with multiple rows with duplicate HGNC symbols due to the nature of converting ENGS to HGNC as expected. However, I’m wondering how…

Between sample normalization without replicates 0 Hi All, I have some RNA-Seq data without reps for 5 different conditions. I can not do any fancy statistics with this data. Just trying to get the idea if the genes of interest show stable expression in these conditions. What is the best…

Between sample normalization with replicates 0 Hi All, I have some RNA-Seq data without reps for 5 different conditions. I can not do any fancy statistics with this data. Just trying to get the idea if the genes of interest show stable expression in these conditions. What is the best…

salmon output interpretation 0 Hi salmon users, Can someone help me interpret salmon output? I ran salmon with one short read sample and see most of its TPM level is 0. I see 150653 among, 252045 is 0. Does this mean, for this specific sample, it’s relative transcript abundance is…

Miles JH. Autism spectrum disorders-a genetics review. Genet Med. 2011;13:278–94. Article  PubMed  Google Scholar  Betancur C. Etiological heterogeneity in autism spectrum disorders: more than 100 genetic and genomic disorders and still counting. Brain Res. 2011;1380:42–77. Article  CAS  PubMed  Google Scholar  Satterstrom FK, Kosmicki JA, Wang J, Breen MS, De Rubeis…

Edelmann L, Pandita RK, Morrow BE. Low-copy repeats mediate the common 3-Mb deletion in patients with velo-cardio-facial syndrome. Am J Hum Genet. 1999;64:1076–86. Article  CAS  PubMed  PubMed Central  Google Scholar  Shaikh TH, Kurahashi H, Saitta SC, O’Hare AM, Hu P, Roe BA, et al. Chromosome 22-specific low copy repeats and…

long read + salmon? (transcript abundance) 2 Hi all, Are there any tools that can quantify transcript abundance (e.g. TPM) from long read? As far as I know, salmon only works with short read data. salmon read long • 63 views • link updated 1 hour ago by Rob 5.8k…

Hi guys, Here’s an RNAseq-related question. I have RF library, I made de novo transcriptome assembly in Trinity with basic parameters and a library flag set to RF. I ran Salmon and got a Mapping rate = 92.5671%. I wanted to check json file and what confused me was the…

Accurate taxonomic identification is foundational for effective species monitoring and management. When visual identifications are infeasible or inaccurate, genetic approaches provide a reliable alternative. However, these approaches are sometimes less viable (e.g., need for near real-time results, remote locations, funding concerns, molecular inexperience). In these situations, CRISPR-based genetic tools can…

How do one analyze data from SMART-Seq stranded kit (v4)? 1 Hi, Can someone please point me to a tutorial or workflow to analyze SMART-Seq data from stranded single-cell RNA? As I am not sure how to map the data or do the downstream analysis. thanks in advance Assa single-cell…

Salmon TPM calculation constant 1 Hi all, salmon seems to calculate the TPM using the equation below, and looks like the constant is 26.1 for every calculated TPM. Does anybody know what this constant means and how it’s derived? TPM = constant * NumReads / EffectiveLength, salmon TPM • 44…

RNA-Seq analysis using STAR and Salmon 2 Hello! I am having some trouble figuring out how to use Salmon. I have around 30 different samples which I trimmed using bbmap then aligned them using STAR. I have all of the BAM files from this alignment. Should I merge them all…

Intron retention gene expression using salmon 0 I have a list of intron retention found in my short read data. I want to see if those intron retentions are lowly expressed. Can somebody comment on my experiment step if this is correct? Run my data (bam file) using salmon Sum…

Zhang J, Liu Y, Zhang N, Hu B, Jin T, Xu H, et al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat Biotechnol. 2019;37:676–84. Article  CAS  PubMed  Google Scholar  Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. Going back to the roots:…

-All Dates- Thursday, February 16 Friday, February 17 Saturday, February 18 Sunday, February 19 Monday, February 20 Tuesday, February 21 Wednesday, February 22 …

Hallegraeff, G. M. Ocean climate change, phytoplankton community responses, and harmful algal blooms: A formidable predictive challenge 1. J. Phycol. 46, 220–235 (2010). Article  CAS  Google Scholar  Itakura, S. & Imai, I. Economic impacts of harmful algal blooms on fisheries and aquaculture in western Japan—An overview of interannual variability and…

Pantel, K. & Alix-Panabières, C. Liquid biopsy and minimal residual disease—Latest advances and implications for cure. Nat. Rev. Clin. Oncol. 16(7), 409–424. doi.org/10.1038/s41571-019-0187-3 (2019). Article  CAS  PubMed  Google Scholar  Pantel, K. & Brakenhoff, R. H. Dissecting the metastatic cascade. Nat. Rev. Cancer 4, 448–456 (2004). Article  CAS  PubMed  Google Scholar …

In December and January, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-nine new annotations in RefSeq for the following organisms: Acinonyx jubatus (cheetah) Anopheles cruzii (mosquito) Anopheles moucheti (mosquito) Bicyclus anynana (squinting bush brown) Budorcas taxicolor (takin) Carassius gibelio (silver crucian carp) Citrus sinensis (sweet orange) Crassostrea angulata (Portugese oyster) Culex pipiens pallens (northern…

Hi. I am working with a mutant library. It is not RNAseq but the idea is more or less the same. I exposed the mutant library to an antimicrobial compound and I collect samples at different times. After that I extracted the DNA, tagged the pools and I sequenced the…

DOI: 10.18129/B9.bioc.rnaseqDTU     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see rnaseqDTU. RNA-seq workflow for differential transcript usage following Salmon quantification Bioconductor version: 3.14 RNA-seq workflow for differential transcript usage (DTU) following Salmon quantification. This workflow uses Bioconductor packages tximport, DRIMSeq, and…

Using salmon on HISAT2 BAM files for transcript quantification 1 Hi, I am wondering if there is any need to align data at all if the goal is to quantify transcripts with salmon. Are there any advantages to aligning versus doing direct. quantification using salmon, since both options seem to…

Which input file is used for DGEList in EgdeR? 1 @mohammedtoufiq91-17679 Last seen 1 day ago Qatar Hi, I used an nf-core/rnaseq pipeline using star_salmon default aligner, on strand specific dataset. I have a question about gene counts data obtained as a result of salmon quantification. I am interested in…

How to map and annotate gene symbols to gene type? 1 Hi, I am working with total RNA-Seq dataset and aligned fastq files against hg38 using STAR and quantified using salmon. Now I am interested in annotating each gene symbol with gene type annotations (for instance; whether the gene is…

The companies Asimov, BioRay Pharmaceuticals and Colossal Biosciences bagged the biggest biotech investments in January 2023. Around the world, synthetic biology players and firms developing treatments for hormonal disorders attracted the biggest funding rounds. 2023 began with a bang in terms of biotech funding, and there are signs of stabilization…

Seilacher, A. Arbeitskonzept zur konstruktions-morphologie. Lethaia 3, 393–396 (1970). Google Scholar  Seilacher, B. A., Reif, W.-E. & Westphal, F. Sedimentological, ecological and temporal patterns of fossil Lagerstätten. Philos. Trans. R. Soc. Lond. B 311, 5–23 (1985). ADS  Google Scholar  Gibbons, N. E. & Reed, G. B. The effect of autolysis…

isoform compostion (psi) question 0 Here are my couple thoughts what I am trying to figure out. I want to estimate the proportion of isoforms (psi) in a biological sample given RNA seq data. Basically I’m trying to simulate a psi value. What would be a good way to know…

SALMON Index build Process Killed! 0 Hello, I was trying to create an decoy-aware index with Salmon (v1.4.0). So I used primary-assembly genome file and transcript file from Gencode library and followed the steps mentioned in the combine-lab.github.io/alevin-tutorial/2019/selective-alignment. Concatenated transcript file with genome to create gentrome.fa.gz. Then tried to create…

Hello, Apologies for a pretty elementary question. I tried my best to answer it using resources online but I find many tutorials/explanations out there difficult to understand. I am trying to quantify human rnaseq data using salmon. The reason I am using salmon is because I would like to perform…

What is Mesotherapy and In Which Situations Is It Applied? Plastic, Reconstructive and Aesthetic Surgeon Op.Dr.Celal Alioğlu gave important information on the subject. Is cross-linked hyaluronic acid injection, one of today’s popular medical aesthetic procedures, as it is known, youth vaccines really effective? Among the products we call youth vaccine,…

Yes, this can well be an I/O problem. The sort will produce lots of intermediate files and merging them requires (obviously) to access them all more or less in parallel, that is something that HDD drives in general, and external ones in particular are slow at. The only way to…

Normalizing Salmon output count data matrix using DESeq2 1 @7cabb0d9 Last seen 12 hours ago United States I import counts and abundance matrix from Salmon output using tximport. I want to normalize the Salmon output count matrix using DESeq2 package. What code should I use to achieve this task? Can…

Expression level of mutant genes in RNAseq data 1 Hello, I have WES data from matched tumor and normal samples and mutants called from these data (in MAF files). From my understanding, if I sequence the tumor sample RNA, and run a routine RNAseq data analysis pipeline, the counts I…

Manually adding genes of interest to transcriptome for RNASeq DE? 1 I have been given some RNASeq reads by a collaborator and have been asked to assess whether there is differential expression between treatments in 6 genes of interest to my collaborator. Unfortunately, this is a non-model organism and so…

Animal and ethics A total of 190 dogs, comprising both healthy dogs (n = 76) and dogs with respiratory symptoms (n = 114), were included in this study. The research assessed nasal swab (NS) and oropharyngeal swab (OS) collected between January and November 2020. The samples from the healthy group were collected from clinically…

Publications PubMed=1260746Drewinko B., Romsdahl M.M., Yang L.Y., Ahearn M.J., Trujillo J.M.Establishment of a human carcinoembryonic antigen-producing colon adenocarcinoma cell line.Cancer Res. 36:467-475(1976) PubMed=7104989; DOI=10.1016/0165-4608(82)90076-0Chen T.-R., Hay R.J., Macy M.L.Karyotype consistency in human colorectal carcinoma cell lines established in vitro.Cancer Genet. Cytogenet. 6:93-117(1982) PubMed=3335022Alley M.C., Scudiero D.A., Monks A., Hursey M.L.,…

Patrick Murphy Bulk RNA-Seq – HackMD        owned this note   Published Linked with GitHub — title: ‘Patrick Murphy Bulk RNA-Seq’ disqus: hackmd — Patrick Murphy bulk RNA-Seq Analysis === ## Table of Contents [TOC] ## 1. Introduction This is a bulk RNA-Seq project, which includes human data….

Hello everyone I have multiple bulk RNA-seq datasets that I need to apply the same pipe line on. I want to normalize them from counts data to TPM. In all datasets, I have the genes as rows, and samples as columns. Unfortunately, I don’t have the fastq files, all I…

Photo of former University of Maine graduate student Mitch Paisker releasing a female Arctic charr that was captured, tagged and measured back into Floods Pond in 2018.Photo by Bradley Erdman. University of Maine and University of New Hampshire researchers will investigate how the diversity and evolution of feeding habits among…

Arlinghaus, R. et al. Governing the recreational dimension of global fisheries. Proc. Nat. Acad. Sci. USA 116, 5209–5213 (2019). CAS  PubMed  PubMed Central  Article  Google Scholar  Cowx, I. G. & Gerdeaux, D. The effects of fisheries management practises on freshwater ecosystems. Fish. Manag. Ecol. 11, 145–151 (2004). Article  Google Scholar …

An international team of scientists primarily based out of the John Innes Centre in the United Kingdom has used gene-editing to create a vitamin D-enriched tomato. Using CRISPR-Cas9, they switched off an enzyme in tomatoes that ordinarily prevents the molecular forerunner of vitamin D3 (called 7-dehydrocholesterol, or 7-DHC) from accumulating…

This is a much more complicated question than it might seem. First, you need to understand how RNA-Seq works, and what your data really is. Your “paired-end files” contain reads, which will contain fragments of transcripts. Since those are only fragments of transcripts, you don’t know what frame they are…

Can Differential Isoform expression analysis can be performed using DESeq2 package 0 @03ddb485 Last seen 9 hours ago India Hello, I am want to perform differential isoform expression (DIE) analysis for RNAseq data from human. Can I use DESeq2 for this by inputting the transcript level abundance and getting differential…

Validate RNAseq salmon quantification pipeline 1 Hi, I’ve written a pipeline to perform quantification from RNAseq data with salmon. I’m trying to find a way to evaluate the quality of my results. I was thinking to run the pipeline on available public dataset and compare my output with another analysis….

DESeq2 on allelic reads 1 @ea088d93 Last seen 26 minutes ago Canada Hello, Can I use DESeq2 to perform differential gene expression on allelic reads? I have allelic reads quantified for each parental allele/copy I have 2 treatments (control vs ethanol-exposed) I want to perform differential gene expression to see…

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

#1008368 – pigx-rnaseq: FTBFS: configure: error: R package rmarkdown not found. – Debian Bug report logs Reported by: Lucas Nussbaum <lucas@debian.org> Date: Sat, 26 Mar 2022 21:12:04 UTC Severity: serious Tags: bookworm, ftbfs, sid Found in version pigx-rnaseq/0.0.19-2 Reply or subscribe to this bug. Toggle useless messages Report forwarded to…

Hi everyone. I am executing Salmon in Galaxy in order to carry out gene quantification from mouse RNA-Seq data (6 samples). To do so, I am providing a reference genome (cDNA, in fasta format), the processed reads (in fastqsanger.gz format) of one of these samples (after executing Trim-Galore) and a…

First, trimming adapters is definitely necessary as they are essentially a form of contamination. For quality trimming and filtering I would highly recommend reading the following: Trimming of sequence reads alters RNA-Seq gene expression estimates Essentially they show that aggressive trimming is a problem. To quote from the Conclusions: The…

Hi everyone, first time working with mouse samples and unfortunately, there are fewer resources available for the latest mouse Ensembl genome than I was expecting. What I’ve done: I performed rRNA depletion on total RNA extracted from mouse tissue and created Illumina libraries using a cDNA synthesis kit with random…

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