Tag: hisat2

Moderate Mapping percentage 1 Hi all, I received my sequenced transcriptome and genomic data from my service provider and started working with it. Both the DNA and RNA data passed quality metrics post trimming. But the mapping percentage comes out to be 90% using bowtie-DNA and 85% using Hisat2-RNA. I…

Animals and samples The study included 10 pigs, 8 pigs were bred at the INRAE experimental farm (doi.org/doi.org/10.15454/1.5572415481185847E12) and 2 pigs come from breeding organizations in accordance with the French and European legislation on animal welfare. The animals belong to the same family, except for one LW animal. Animals were…

Introduction Combined allergic rhinitis and asthma syndrome (CARAS), a new terminology introduced by the World Allergy Organization (WAO) in 2004, is an allergic reaction that occurs in the respiratory tract, including upper respiratory tract allergy (allergic rhinitis, AR) and lower respiratory tract allergy (asthma, AS).1,2 The incidence of AS in…

This is a guide for preparing for importing RNA-Seq FASTQ files to Subio Platform on a Mac computer. If you use a Windows10 machine, please go to the guide for Windows10. Subio Platform utilizes the following tools to process the RNA-Seq FASTQ files. fastp to trim adapters and filter low-quality…

Dobson, G. E. On a new genus and species of Rhinolophidae, with description of a new species of Vesperus, and notes on some other species of insectivorous bats from Persia. J. Asiat. Soc. Bengal. 40, 455–461 (1871). Google Scholar  Bates, P., Bumrungsri, S., Francis, C., Csorba, G. & Furey, N….

Boukouvala, M. C. et al. Lymantria dispar (L.) (Lepidoptera: Erebidae): Current Status of Biology, Ecology, and Management in Europe with Notes from North America. Insects 13 (2022). Keena M. A., Richards, J. Y. Comparison of Survival and Development of Gypsy Moth Lymantria dispar L. (Lepidoptera: Erebidae) Populations from Different Geographic…

Merge overlapping paired end reads from BAM file. 0 Hi everyone, Using Trimmomatic and then HISAT2, I have aligned 300 RNA fastq samples (NovaSeq6000, RNA sequencing, paired-end, 150bp sequencing). I have found a percentage of overlapping paired end reads (read through) in the 300 .bam files. I found the overlaps…

Hello Biostars, I am looking for some guidance on how to merge some files for my rna-bulk sequencing analysis. Let me start by describing the problem: I recieved an mRNA sequence of 4775 characters which I would like to merge with the human reference genome that I download from NCBI…

Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS  PubMed  PubMed Central  Google Scholar  Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…

Datasets To avoid the so-called ‘dataset bias’20,that some datasets are generated with specific structures and thus the results are ‘over-optimistic’ (in the case of working with our novel method), we performed the analysis in the light of several real datasets (see Table 4). We used four different datasets from the NCBI…

Hello everyone, I am stuck trying to analyze some single-end RNAseq data from human tissue. My issue is that the alignment with HISAT 2 went very well: 94.95% overall alignment rate. However, when I use featureCounts, I get: 5.7% when I set the strandSpecific parameter to 1. 5.3% when I…

Friedman-Einat, M. & Seroussi, E. Avian leptin: bird’s-eye view of the evolution of vertebrate energy-balance control. Trends Endocrinol. Metab. 30, 819–832 (2019). Article  CAS  PubMed  Google Scholar  International Chicken Genome Sequencing C. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716 (2004)….

Strandedness of RNA-seq results 1 Hi all, I am not very familiar with bioinfo things as my background is more towards wetlab. I am analysing my dual RNA-seq results (host+pathogen RNA), and I am using HISAT2 (aligned to genome) + featurecounts pipeline. I am not sure why I only get…

Annotation GTF/GFF Arabidopsis thaliana 0 Hello, this is my first time working with Arabidopsis and I am quantifying with featureCounts as follows: featureCounts -p –countReadPairs -t exon -g gene_id -a ../genome_arabidopsis/Arabidopsis_thaliana.TAIR10.57.gtf -o SRR14059988.txt ../alignment_hisat2/SRR14059988_sorted.bam However, in my counts I am having counts associated with long non conding, ribosomals, mitochondrial and…

Can’t install hisat2 with miniconda 0 I’ve been trying to install hisat2 with Miniconda but I keep getting this error. Miniconda is updated and seemingly installed. Also I’m on Mac OS. Please Advise. Channels: bioconda default defaults conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): done Solving environment: failed PackagesNotFoundError: The…

New BMC Bioinformatics Paper on “Transformer-based tool recommendation system in Galaxy” Abstract: Background: Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses in Galaxy. Tool recommender system predicts a collection of tools that can be used to extend…

Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article  ADS  CAS  Google Scholar  Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…

Kumar A, Rasche H, Grüning B, Backofen R. Tool recommender system in Galaxy using deep learning. GigaScience. 2021. doi.org/10.1093/gigascience/giaa152. Article  PubMed  PubMed Central  Google Scholar  The galaxy community: the galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res 50(W1):W345-W35104 2022. (2022). doi.org/10.1093/nar/gkac247 Gil Y, Ratnakar…

Hello everybody. I’m a newbie in RNA-seq Analysis, and I have this situation that I don’t really understand. While working with featureCounts for RNA-seq read quantification, I came across an intriguing issue. The rate of successfully assigned alignments turned out to be unexpectedly low, totalling just 15463270 (7.6%). This was…

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…

Introduction The development of multicellular organisms requires the activation of different gene batteries which specify the identity of each individual cell type. Such shifts in cellular identity are driven by shifts in the gene regulatory network (GRN) consisting of transcription factors (TFs) binding to the enhancers and promoters of their…

Ethics statement All mice procedures in this study were performed under an animal protocol approved by the Institutional Animal Care and Use Committee guidelines of Westlake University. The procedures and protocols for glioma patients were approved by the institutional review board of Beijing Tiantan Hospital. Informed consent was obtained from…

hisat2-build 0 Hello, I am running this command on my reference genome found www.ncbi.nlm.nih.gov/datasets/genome/GCF_003957565.2/ hisat2-build -p 16 /Volumes/cachannel/ZebraFinchBrain/GCF_003957565.2/ncbi_dataset/data/GCF_003957565.2/GCF_003957565.2_bTaeGut1.4.pri_genomic.fna /Volumes/cachannel/ZebraFinchBrain/reftwo/referencegenome2 However I get this error where no A nucleotides are counted. This is odd because in the .fna file it is clear that they are present. Returning block of 12034714 for…

Hello, I have ran htseq-count numerous times and continue to get the same error. That NONE of my genes are counted as seen here. ZXDC 0 ZYG11B 0 ZYX 0 ZZEF1 0 ZZZ3 0 __no_feature 70257177 __ambiguous 0 __too_low_aQual 1509790 __not_aligned 3970775 __alignment_not_unique 4277765 However, I have a very high…

Snap frozen Postnatal day4 murine kidney tissues were crushed using micropestles in RLT Buffer and RNA was extracted from these tissues using QiaShredders followed by Qiagen RNAeasy Mini Kits according to manufacturer’s protocol. RNA concentration and integrity were determined by Aligent bioanalyzer. cDNA library preparation was carried out using NEB…

RNA-Seq with DNA contamination, any way to salvage the data? 1 Hello, My group has performed RNA-Seq using Illumina Truseq RNA Exome kit, we performed alignments with HISAT2 and we noticed that a good portion of our samples had DNA contamination. So far, I have seen a lot of discussion…

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…

Nematode materials and species identification Mi, Mj, and Mg were collected from farmlands in Wuhan city of Hubei province, Longyan city of Fujian province, and Changsha city of Hunan Provinces, respectively. Two Ma samples were collected from farmlands in Shenyang city of Liaoning province and Shiping city of Yunnan province….

Cancer Genome Atlas Research, N. Integrated genomic characterization of papillary thyroid carcinoma. Cell 159, 676–690. doi.org/10.1016/j.cell.2014.09.050 (2014). Sherman, S. I. Thyroid carcinoma. Lancet 361, 501–511. doi.org/10.1016/s0140-6736(03)12488-9 (2003). Article  PubMed  Google Scholar  Tong, J. et al. Poorly differentiated thyroid carcinoma: a clinician’s perspective. Eur. Thyroid J. 11, doi.org/10.1530/ETJ-22-0021 (2022). Asioli, S….

zero counts for all genes in RNAseq data of Ferret 0 I have bulk RNAseq data from Ferret and trying to get counts per gene. to do so I used hisat2 and got the genome from here: hgdownload.soe.ucsc.edu/goldenPath/musFur1/bigZips/musFur1.2bit after aligning the fastq files I used htseq and the following command:…

Introduction The non-random packaging of chromatin within the nucleus is a universal feature of eukaryotic genomes. The three-dimensional (3D) spatial organization of chromatin could be partitioned at different levels based on the interaction frequency between two given loci in the genome. Advances in sequencing technologies have led to the identification…

Bacterial strains and phages Escherichia coli DH5a was routinely grown in Lysogeny broth (LB) medium and used for plasmid cloning, while E. coli BL21 (DE3) was used for protein production and the in vivo assays. E. coli phages T5, T7 and Lambda-vir are gifts from Shi Chen lab (Wuhan University,…

Samtools filtering based on PNEXT 0 Hi all, I was wondering if I’m missing something obvious: samtools can filter your BAM file based on many criteria (such as flags, tags, qlen etc) – but what is the correct way to get rid of the chimeric mappings (at least the type…

Mushroom collecting Sporocarps were collected from various herbaria and during three expeditions to Point Reyes National Seashore (PRNS), California in 2004, 2014 and 2015, and in 2015 from three sites in Portugal. A total of 86 sporocarps were collected: 67 Californian sporocarps (one early herbarium sample dates to 1993), 11…

Aguilera F, McDougall C, Degnan BM (2017) Co-option and de novo gene evolution underlie molluscan shell diversity. Mol Biol Evol 34(4):779–792 CAS  PubMed  PubMed Central  Google Scholar  Alexa A, Rahnenfuhrer J (2020) topGO: Enrichment analysis for gene ontology. R package version 2.40.0 Google Scholar  Arivalagan J, Yarra T, Marie B,…

How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols 0 My RNAseq analysis pipeline is as follows: fastqc (read quality is good, some overrepresentation of adaptor sequence) -> trimmomatic (trimmed adaptor sequence, qc report after trimming suggests the overrepresented adaptors are gone) ->…

Hisat2-build (5.ht2 and 6.ht2 are missing) 0 Hi all, I am trying to index the reference.fasta file using hisat2/stringtie. First I want to index the genome using hisat2. (>hisat2-build ref.fa ref) The manual states that 8 files should be produced after indexing 1.ht2 to 8.h2t. However, I only have six…

How do mRNASeq, BulkRNASeq, and TotalRNASeq differ in terms of workflow? 0 I want to look for differential gene expression a dataset from a collaborating lab. I have successfully done end-to-end analysis for mRNASeq, CHIPSeq and ATACSeq but I’m very confused about analyzing BulkRNASeq and TotalRNASeq. How different is the…

hisat2 index file error 1 hi dear i do hisat2 -q -x ../hg38/*.ht2 -1 SRR23132814_1_trim.fastq -2 SRR23132814_2_trim.fastq –add-chrname -S SRR23132814.sa and also i do hisat2 -q -x //wsl.localhost/Ubuntu-22.04/home/alikian/RNAseqData/hg38/*.ht2 -1 SRR23132814_1_trim.fastq -2 SRR23132814_2_trim.fastq –add-chrname -S SRR23132814.sa but i see this error (ERR): “../hg38/genome.1.ht2” does not exist Exiting now … or this…

Hi everyone, I hope you’re doing well. I’ve been encountering a puzzling issue in my RNA-seq analysis pipeline and was hoping to get some insights from this knowledgeable community. I’m currently working on an RNA-seq project, where I’ve aligned my trimmed reads to the mouse reference genome (GRCm39) using HISAT2…

Introduction Chronic obstructive pulmonary disease (COPD) is a condition that is characterized by persistent respiratory symptoms and airflow limitations that are not fully reversible. The severe complications of the disease may adversely affect its morbidity and mortality.1 According to World Health Organization (WHO) statistics, over 3 million people per year…

Murchison, E. P. Clonally transmissible cancers in dogs and Tasmanian devils. Oncogene 27, S19–S30 (2009). Article  Google Scholar  Metzger, M. J. & Goff, S. P. A sixth modality of infectious disease: contagious cancer from devils to clams and beyond. PLoS Pathog. 12, e1005904 (2016). Article  PubMed  PubMed Central  Google Scholar …

Comparing RNASeq data from multiple studies 0 @5576e7cd Last seen 1 hour ago United States I am looking to compare RNASeq results from 3 different studies that have uploaded their data to repositories. However, study 1 uploaded the raw fastq files, study 2 uploads raw mapped counts or normalized counts…

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…

The file name format is like this: 4digitnumber_S_R1_001.fastq.gz. To give you an example 3145_S2_R1_001.fastq.gz I’m trying to have my output file name not include _R1_001 part but it keeps including the full file name. I am not sure why it’s not giving me the correct output file name format that…

Hisat2 index and alignment question 0 I indexed my reference genome using hisat2-build (mus musculus) and got 8 index files. However when I tried to start my alignment in the directory of my fastq files using this command hisat2 -p 8 -x /path/to/musculus_index -1 SRR8348941_1_P.fastq.gz -2 SRR8348941_2_P.fastq.gz -S SRR8348941.sam –dta-cufflinks…

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…

Introduction Single-cell RNA sequencing (RNA-seq) was first achieved by using a quantitative cDNA amplification method and applied to mouse oocytes (Kurimoto et al, 2006; Tang et al, 2009). It has since provided unprecedented opportunities for the study of cellular differentiations, states, and diseases in various biological fields, including developmental biology,…

Introduction COPD, a common preventable and treatable disease characterized by persistent airflow limitation and respiratory symptoms, is associated with exposure to harmful environments. COPD is currently the third leading cause of death globally. The high incidence and mortality of COPD, which seriously threaten human health, represent a public health problem…

Job Description About the Job The Research Informatics (RI) Bioinformatics group within the University of Minnesota Supercomputing Institute (MSI) is hiring a full-time Bioinformatics Analyst to support research for the Department of Microbiology and Immunology (MI) at the University of Minnesota. The analyst in this position will conduct cutting-edge bioinformatics…

Hello all, I was just wondering what a reasonable percentage of ‘novel’ splice junctions/splice events is for human RNAseq data using the program junction_annotation.py. I am new to RNAseq and just running some published human RNAseq data through my pipeline in order to familiarize myself with the programs and protocols….

About the Job The Research Informatics (RI) Bioinformatics group within the University of Minnesota Supercomputing Institute (MSI) is hiring a full-time Bioinformatics Analyst to support research for the Department of Microbiology and Immunology (MI) at the University of Minnesota. The analyst in this position will conduct cutting-edge bioinformatics analyses in…

Enrichment analysis guide for msu7 rice genome 0 Hi everyone, i’ve been following through the hisat2-strintie-deseq2 pipeline for my samples using the msu7 rice genome as the reference (rice.uga.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/). Now that the alignment process is done, the gene_id looks like this: LOC_Os06g17030 LOC_Os11g01380 LOC_Os05g38810 LOC_Os01g43480 After Deseq2 analysis i have…

Filtering parasite reads from host reads 0 Hi all, I have RNA-seq PE fastq reads for control and infected (at different time points) samples. The host species is lacking a reference genome. Thus, I will be doing a de novo transcriptome assembly and later differential gene expression analysis. My questions:…

Harley, R. M. et al. Labiatae. in Flowering Plants · Dicotyledons. The Families and Genera of Vascular Plants (ed. Kadereit, J. W.) vol. 7 167–275 (2004). Kokkini, S., Karousou, R. & Hanlidou, E. HERBS | Herbs of the Labiatae. Encyclopedia of Food Sciences and Nutrition 3082–3090 (2003) doi.org/10.1016/B0-12-227055-X/00593-9. Hao, D….

HISAT2 HLA genotyping errors 2 Hi,I’m trying to follow the tutorial for HLA typing and assembly in HISAT2 as described at ccb.jhu.edu/hisat-genotype/index.php/Type:HLA using my own RNAseq data. I do everything as described. I have samtools 1.7 installed. I am able to extract my HLA reads. But when I get to…

Soltis, P. S. & Soltis, D. E. Polyploidy and Genome Evolution (Springer, 2012). Chen, J. Z. & Birchler, J. A. Polyploid and Hybrid Genomics (Wiley-Blackwell, 2013). Ye, C. Y. et al. The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Mol. Plant 13, 1298–1310…

The Research Informatics (RI) Bioinformatics group within the University of Minnesota Supercomputing Institute (MSI) is hiring a full-time Bioinformatics Analyst to support basic biomedical and applied clinical genetic research for the Department of Laboratory Medicine and Pathology (LM&P) at the University of Minnesota. The analyst in this position will…

How to convert original BED file to a GTF ? 1 Hello everyone, Now, I use Linux base for analyse HISAT2, Stringtie, ballgown. I have the original BED file and I would like to convert to GTF file for Stringtie analysis. If you have some suggestion about tool Or command…

High discordant alignment with HISAT2 Mus musculus 0 I ran HISAT2 on my reads post adaptor removal, and received very high discordant alignments (>80%) with low concordant alignments. 81987410 reads; of these: 81987410 (100.00%) were paired; of these: 81584433 (99.51%) aligned concordantly 0 times 92014 (0.11%) aligned concordantly exactly 1…

Key plasmids used in this study Construction details for all vectors are provided in Supplementary Table 1. Key plasmids included (1) a constitutive KEAP1 expression vector (pJH1004, PhCMV-KEAP1-pA) and the corresponding vector containing inverted terminal repeats (ITRs) of Sleeping Beauty (SB) transposase (pJH1054, ITR-PhCMV-KEAP1-P2A-BlastR-pA-ITR) for stable cell line generation; (2)…

O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion and functional annotation. Nucleic Acids Res. 44, D733–D745 (2016). Google Scholar  Frankish, A. et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 51, D942–D949 (2023). Google Scholar  Pertea,…

Tumor samples from patients Biopsies of primary breast tumors and breast tumors that had metastasized to the brain were obtained from patients with TNBC at the National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital of the Chinese Academy of Medical Sciences and Peking Union Medical College. Single-cell RNA sequencing…

Read groups in RNA-seq 0 Hi bioinformaticians, If I have paired end reads for my samples and I am looking to perform alignment either using HISAT2 or STAR, will the alignment results change significantly depending on whether the reads are separately aligned based on read groups (merged subsequently), or if…

Quach TT, Honnorat J, Kolattukudy PE, Khanna R, Duchemin AM. CRMPs: Critical molecules for neurite morphogenesis and neuropsychiatric diseases. Mol Psychiatry. 2015;20:1037–45. Article  CAS  Google Scholar  Moutal A, White KA, Chefdeville A, Laufmann RN, Vitiello PF, Feinstein D, et al. Dysregulation of CRMP2 post-translational modifications drive its pathological functions. Mol…

Bourque, G. et al. Ten things you should know about transposable elements. Genome Biol. 19, 199 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Chuong, E. B., Elde, N. C. & Feschotte, C. Regulatory activities of transposable elements: from conflicts to benefits. Nat. Rev. Genet. 18, 71–86 (2017). Article  CAS …

Hello I am doing a transcriptome analysis on Pseudomonas putida and I have been trying to do a read count using Htseq -count. The program always give an error. I have tried different genome references (fna) and annotation files (gtf ang gff) but it does not work. The mapping works…

Interpreting Hisat2 alignment output 1 I am am aligning my RNAseq data to a reference genome using Hisat2 for the first time and I have what I am sure is a basic question. However I am still confused after reading a number of online resources. Broadly, my pipeline goes from…

Hayes, C. Cellular immunotherapies for cancer. Ir. J. Med. Sci. 190, 41–57 (2021). Article  PubMed  Google Scholar  Laskowski, T. & Rezvani, K. Adoptive cell therapy: living drugs against cancer. J. Exp. Med. 217, e20200377 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  June, C. H., O’Connor, R. S., Kawalekar, O….

bismark bowtie2 path error 0 Hi, I’m encountering an error while running the bismark command in windows10. I’ve completed the genome preparation step and now I’m trying to run the following command: perl D:\bismark\Bismark-0.24.1\bismark.pl –path_to_bowtie2 D:\bismark\bowtie2-2.5.1-mingw-x86_64 –genome D:\bismark\genome and I’m getting this error: The system cannot find the path specified….

Kamoun, S. et al. The top 10 oomycete pathogens in molecular plant pathology. Mol. Plant Pathol. 16, 413–434 (2015). Article  PubMed  Google Scholar  Derevnina, L. et al. Emerging oomycete threats to plants and animals. Philos. Trans. R. Soc. Lond. B Biol. Sci. 371, 20150459 (2016). Yang, X., Tyler, B. M….

Position Title: Bioinformatics Analyst, UB Genomics & Bioinformatics CorePosting Number: R230011Employer: Research FoundationSalary Range: $50,000 – $55,000FTE: 1.00Position SummaryThe University at Buffalo, Department of UB Genomics and Bioinformatics (ubnextgencore.buffalo.edu/) is seeking candidates for the position of Bioinformatics Analyst. The Bioinformatics Analyst is responsible for supporting the ever-growing computational analysis needs…

I have seen a lot of misinformation in this thread about Mac M1 systems. I feel the need to address these as an new answer rather than a comment. First, I have yet to see a command line tool that did not run on M1. Perhaps those with GUIs do…

Gaucherand, L. & Gaglia, M. M. The role of viral RNA degrading factors in shutoff of host gene expression. Annu. Rev. Virol. 9, 213–238 (2022). Article  PubMed  Google Scholar  Bercovich-Kinori, A. et al. A systematic view on influenza induced host shutoff. eLife 5, e18311 (2016). Article  PubMed  PubMed Central  Google…

Analize RNA-seq data using Hisat2 0 Hi all, I’m trying to analyze RNA-seq data. I performed paired-end sequencing and to prepare the libraries I have used Illumina Stranded mRNA Prep, so my reads are stranded. After quality check I used Hisat2 to perform the alignment and I selected the option…

How to to lncRNA analysis from WTS data ? 0 Hi, I have WTS data with me and I have to do mRNA analysis, lncRNA analysis etc. using the data. Until now what I have done is map the pre-processed data to reference genome using Hisat2 and do quantification using…

Position Title: Bioinformatics Analyst, UB Genomics & Bioinformatics CorePosting Number: R230011Employer: Research FoundationSalary Range: $50,000 – $55,000FTE: 1.00Position SummaryThe University at Buffalo, Department of UB Genomics and Bioinformatics (ubnextgencore.buffalo.edu/) is seeking candidates for the position of Bioinformatics Analyst. The Bioinformatics Analyst is responsible for supporting the ever-growing computational analysis needs…

Hi all, I am working with the RNA-seq data on humans (24patients-20controls). I used DESeq2 to find differentially expressed genes. here is the code that I used: It is corrected for cell-type composition (using cibersort and PCA on the estimated cell-type proportions) dds <- DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=folder, design=~Plate+RIN+Sex+Age+condition+PC2+PC1) #considering PC1,PC2 as…

1. Introduction With the global temperature rise, the dairy industry is confronted with a significant challenge brought about by severely damaging impacts of heat stress. Heat stress increases mortality rates and threatens the health of livestock, especially in highly productive and intolerant species. The increase in ambient temperature–humidity index (THI)…

Ran tin.py in Rseqc, and I got all of the outputs with TIN calculations, but when looking at the error files, many of the lines say “[NOTE:input bed must be 12-column] skipped this line:”. I converted gtf from Ensembl to bed file, and this is the general layout: MT 15725…

How i can get unalignment read in hisat2 ? 0 is there any option in hisat2 for viewing unalignment read? first: i make index for my refrence genome with this command: hisat2-build -p 3 Danio_rerio.GRCz11.cdna.all.fa /home/ngs/zebra_fish second: i make alignment my fastq file with reference genome, using this command: hisat2…

Solving environment: failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: 1 I am trying to install samtools on my environment bioconda with this command: bioconda install samtool I get this error: Solving environment: failed with initial frozen solve. Retrying…

hisat2-align exited with value 1 1 I am a beginner with command and bioinformatics I am trying to alignment with HISAT2 for RNA seq so first I install the HISTA2 by bioconda using this command: bioconda -c install hisat2 after that i made index for my reference genome with this…

Tool:ChatGPT optimized for bioinformatics questions 1 Hey everyone! I launched a new chatbot today that is bioinformatics focused! It’s trained on bioinformatics content and should help debug / ideate much faster for you than vanilla ChatGPT. Check it out here: ai.tinybio.cloud/chat Thanks! gpt • 165 views • link updated 1…

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,…

hisat2 Error 137 0 hi every body, I am running hisat2 with below command: hisat2 –dta -x /home/genetics/apps/Proj/Index/hg38/genom -1 SRR11573854_1P -2 SRR11573854_2P -S SRR11573854.sam -p 4 and I face this error: Killed (ERR): hisat2-align exited with value 137 could you help me to solve this problem? Thank you very much…

The Seibold Laboratory is a cutting-edge, NIH funded, laboratory focused on elucidating the pathobiological basis of asthma and other complex lung and allergic diseases. Our goal is to discover pathobiological subgroups of disease (termed disease endotypes) and the genetic, environmental, and immune factors driving their development. We are accomplishing these…

Hi all, I am working with the RNA-Seq data on human (24Cases-20 controls) to find differentially expressed genes. my RNA-Seq data is unstranded. Here is the comments that I used to align the fastq files: ls *_1P.fastq.gz | parallel –bar -j8 ‘R2=$(echo {} | sed s/_1/_2/) && out=$(echo {} |…

Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our 35,000 employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of…

Name Last modified Size Description Parent Directory   –   e2t.ctab 2023-04-28 14:22 2.7M   e_data.ctab 2023-04-28 14:22 14M   heart-hisat2_stats.txt 2023-04-28 13:58 647   heart.cov_refs.gtf 2023-04-28 14:22 5.4M   heart.gtf 2023-04-28 14:22 38M   heart.sorted.bam 2023-04-28 14:07 12G   heart.sorted.bam.bai 2023-04-28 14:11 2.0M   heart_checksums.md5 2023-04-28 14:23 484  …

Topic participation The examine protocol was accredited by the ethics committees of Osaka College and associated medical establishments in addition to the Translational Well being Science and Know-how Institute (Faridabad). Japanese people (n = 343) for whom intestine metagenome shotgun sequencing had been carried out in earlier research had been included on…

Subject participation The study protocol was approved by the ethics committees of Osaka University and related medical institutions as well as the Translational Health Science and Technology Institute (Faridabad). Japanese individuals (n = 343) for whom gut metagenome shotgun sequencing were performed in previous studies were included in this study46,47,48. Among these…

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…

No differentially expressed genes after multiple testing correction in mice 0 Hi all, I am working with the RNA-seq data on mice (group A N=3 vs group B N=3). Mice are littermates, of which group A overexpresses a human transgene which I verified. I have had .cram files from mouse…

Cell strains E. coli DH5α and B. subtilis 168 strains were grown overnight in Luria-Bertani broth at 37 °C and 180 rpm to a final OD600 ~1.7. B. subtilis strain 168 was kindly provided by Dr. S.A. Dubiley (Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia). T. adornatum strain…

Posting Details Position Information Fiscal Year2022-2023 Position TitleBioinformatics Analyst, UB Genomics & Bioinformatics Core Classification TitleProgrammer/Analyst (Project) DepartmentUB Genomics and Bioinformatics Posting NumberR230011 Posting Link www.ubjobs.buffalo.edu/postings/39824 EmployerResearch Foundation Position TypeRF Professional TypeFull-Time Appointment Term Salary GradeE.79 Posting Detail Information Position Summary The University at Buffalo, Department of UB Genomics and…

Materials The materials used for cell cultures and characterization are listed in Additional file 1: Table S1. Cell sources After getting informed consent, PB was drawn from three healthy O, Rh D-positive donors. CB was collected from three healthy newborn babies at the Department of Obstetrics and Gynecology at Severance…

Multi-mapping read adjacency in alignment tool outputs 0 Hello friends, I often work with SAM/BAM formatted short read alignments in a context where it is beneficial to know all alignments for each read rather than best/primary/secondary. My question: Among short read alignment tools and their configurations, is there ever a…

HISAT2 relaxing parameters? 1 Hi, It’s my first time using HISAT2 and the options have gotten me all confused. How can I run HISAT2 such that I increase the number of mapped reads by relaxing the parameters? Essentially, how can I increase the number of mismatches, etc allowed (which options…