Tag: TSS

  The following is an excerpt from an E-book that Twist developed for Genetic Engineering News: The Changing Landscape of CRISPR Screening: A guidebook to the latest CRISPR screening methodologies and technologies. You can download the full E-book here.   Even for seasoned researchers, designing an sgRNA library can be…

RNA-targeted NBTs that are currently being used to upregulate gene expression address both transcriptional and translational mechanisms and can be roughly divided into two groups: (1) NBTs that increase mRNA abundance by enhancing transcription or increasing mRNA stability (Fig. 3) and (2) NBTs that optimize translation (Fig. 4). Strategies in the first…

DOI: 10.18129/B9.bioc.RcisTarget     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see RcisTarget. RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions Bioconductor version: 3.13 RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list….

We analyzed data from a total of 2,733 participants from the GALA II16 and SAGE17 asthma case–control studies who self-identified as African American (AA; n = 757), Puerto Rican (PR; n = 893), Mexican American (MX; n = 784) or other Latino American (LA; n = 299) (Table 1 and Supplementary Table 1). The median age of the…

Hi, I am a newbie to RNA-seq data analysis. I have to identify differentially expressed genes (DEGs) between human and chimpanzee in a tissue type. I have comparable RNA-seq experiment data (reads/fastq) for the two species. Each species has 2 biological replicates(each with three technical replicates) so six runs per…

Despite being an established model, the genome and annotation of P. tricornutum are not concordant and the existing epigenetic resources generated so far lack a well-defined framework for accurate and user friendly utilization. To address this limitation, we sought to establish a coherent resource rendering the multiple genomic and epigenomic…

BZR1 regulatory network in maize and Arabidopsis. a Distribution of ZmBZR1 binding around transcribed genes. Frequency of ZmBZR1 binding peaks up to 10 kb up- or downstream of TSS or TTS and intra-genic, respectively. b ChIP-seq identified ZmBZR1 binding in proximity of putative targets repressed (BR6ox2/BRD1), induced (IAA19) or not controlled…

doi: 10.1007/978-1-0716-2477-7_26. Memberships Expand Connections 1 Department about Chemical and Systems Biology, Stanford University, Stand-ford, CANCER, USA. [email protected] 2 Department of Chemical and Systems Nature, Stanford University, Stanford, CA, USA. [email protected] Freely PMC article Item in Clipboard Magdalena P Crossley et aluminium. Methods Mol Bil. 2022. Free PMC books Show details…

JAK inhibitors have paved the way and improved clinical outcomes for patients with myeloproliferative neoplasms over the past decade. Not only have these agents shown significant improvements in efficacy outcomes, but they have demonstrated favorable safety profiles in this patient population. Currently, 3 JAK inhibitors are approved for patients with…

hi, I have a question or suggestion for you all. I have some peaks and I would to annotate them. My goal is to extend the annotation 10000 upstream from the start of the gene and 10000 downstream from the end of the gene body. So I don’t want to…

image: Example of a gene that contains two possible start sites (TSS), and two possible end sites (TES). Black boxes in the gene model show sequences that will be translated into protein. With conventional short-read mRNA sequencing, in which signal represents the accumulation of reads, it is not possible to distinguish…

Example of a gene that contains two possible start sites (TSS), and two possible end sites (TES). Black boxes in the gene model show sequences that will be translated into protein. With conventional short-read mRNA sequencing, in which signal represents the accumulation of reads, it is not possible to distinguish…

Hey everyone, I’m currently working on annotating TSS (Transcription Start Site) information, and I have come across a dilemma: should I annotate TSS by transcript or by gene? I would really appreciate your insights and opinions on this matter. On a related note, I have been trying to implement a…

I am trying to get computeMatrix for bigwig file in specific genomic region using deeptools.Below is the code I am using computeMatrix reference-point –referencePoint TSS \ -b 1000 -a 1000 \ -R ~/Desktop/ATAC/ATAC/Inducible_elements_Greenberg.bed \ -S ~/Desktop/ATAC/Control.mRp.clN.bigWig \ –skipZeros \ -o ~/Desktop/ATAC/matrix_controlmRPATACBasalcomputematrix.gz \ But I get the following error File “/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/__init__.py”,…

Development and benchmarking of MEGAnE Accurate variant genotyping is required for statistical genetics. To enable both discovery and accurate MEV genotyping from genomes studied using short reads, we developed a new bioinformatic tool, mobile element genotype analysis environment (MEGAnE; Supplementary Note). Compared to SVs resolved by long reads, MEGAnE discovers…

Enrollment to the phase 3 MANIFEST-2 trial (NCT04603495), which is examining the safety and efficacy of pelabresib plus ruxolitinib (Jakafi) vs ruxolitinib alone in patients with JAK inhibitor–naïve myelofibrosis, has completed and topline findings are anticipated by the end of 2023.1 The multicenter, double-blind, placebo-controlled, trial enrolled patients with primary,…

How to find coordinates of TSS from 5pUTR and TTS from 3pUTR in transcriptome/ mRNA ? 0 Hello Researchers Can you please tell me just the correct coordinates of TSS(1kb) from 5pUTR + & – strand and TTS(1kb) from 3pUTR + & – strand of transcriptome/ mRNA? I only have…

I was wondering if anybody has information on how to choose guides for optimal gene activation/repression using multiplex CRISPR/Cas9s with only two guides? I have tried different combinations e.g. two guides with average activity v.s. one poor guide plus an average guide and got mixed results. Sometimes the latter outperformed…

Retrieve Promoter Sequences by GeneID 0 Hello! I want to retrieve promoter sequences starting from a list of Gene_ID, i had try to used RSAT-retrieve sequence, but the problem is that they retrieve the sequence from the start codon or the stop codon, but i want retrieve the sequence 1500bp…

Nearly 90% of the disease risk-associated variants identified by genome-wide association studies are in non-coding regions of the genome. The annotations obtained by analyzing functional genomics assays can provide additional information to pinpoint causal variants, which are often not the lead variants identified from association studies. However, the lack of…

Download the promoter, enchancer, TSS , 3 prime, exon and intron positions of all hg38 genes 1 Hi All, I would like to download the promoter enhancer, exon, intron, 3’prime, 5’prime positions of all genes from the human genome hg38 version. I have seen a couple of information in the…

use ROSE to identify super enhancer 0 hey everyone, i want to use ROSE to identify super enhancer and to see if there is difference in the super enhancer after some treatment in lung cancer cell line i see that this is the typical use: [user@cn3107 ~]$ ROSE_main.py -h Usage:…

Search for creTA elements associating with I-F CRISPR-Cas Previously identified creTA genes all surround the cas6 gene of a type I or III CRISPR-Cas19. Yet, within the I-F CRISPR-Cas loci of Acinetobacter species, we did not find any creTA-like elements by searching the sequences surrounding csy4 (a subtype-specific cas6 gene)….

Nanopore reads coupled to a novel computational method extends analyses of differential methylation to sparse CpGs (outside CpG islands) We analyzed tumor samples at diagnosis (T) and relapse (R) from three AML patients (UD5, UD10 and AML2) who received standard chemotherapy and relapsed with chemoresistant disease (supplementary Table 1). DNA from…

Multiple H2BNTac sites occupy the same genomic regions H2BNTac sites are similarly regulated by CBP/p30018 (Supplementary Fig. 1a), yet the reported genome occupancy patterns of H2BNTac sites are dissimilar from each other22,23 (Supplementary Note 1). To resolve this conundrum, we systematically compared H3K27ac and H2BNTac genomic occupancy and regulation by…

How to extract the DNA sequence 1000 bp around the Transcription start site (TSS) of a gene symbol in NCBI gene with R? 0 I am trying to extract the DNA sequence 1000 bp around the Transcription start site (TSS) of a gene, and I get a code as follows:…

extract gene coordinates and TSS from gene list 2 Hi, I have a list of 50 genes like this: “Tshz2” “Ebf1” “Col26a1” “Ebf2” “Unc5c” “Prkg1” “Eya1” “Ldb2” “Rbms3” “Arhgap6” And I need the coordinates of gene body and the TSS +1000/-1000 bp. How can I get it on R? The…

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which is otherwise known as the coronavirus disease 2019 (COVID-19), continues to pose significant…

In several manuals (example) on ChIP-seq analysis they pre-select, for instance +1000bp and -1000bp from the TSS as the “promoter-bound” regions: peakAnno_bcl11b <- ChIPseeker::annotatePeak(peak = ‘bcl11b_peaks.narrowPeak’, TxDb=txdb, tssRegion=c(-1000, 1000) ) which produces an object with a slot @anno in which each peak is assigned either “Promoter”, “5’ UTR”, “3’ UTR”,…

Structure-based identification of a small-molecule PAF1 complex (PAF1C) inhibitor that impairs PAF1 chromatin localization and releases RNA Pol II. (A) Schematic representation of the structure-based identification of small-molecule disruptors of PAF1 and CTR9 interactions using in silico screen followed by RNA Pol II ChIP-seq screening. iPAF1C binding residues of CTR9…

pyscenic cannot mapped to the feather file 0 Good afternoon, I am conducting a pyscenic analysis, but I am encountering a problem. Initially, I tried using “hg19-500bp-upstream-10species.mc9nr.genes_vs_motifs.rankings.feather”, but the log file indicated that gene xxx could not map to the feather file. So, I switched to “hg19-tss-centered-10kb-10species.mc9nr.genes_vs_motifs.rankings.feather”. However, I am…

I have seen many many papers mentioning “GENCODE TSS” However, upon looking at the GENCODE GTF file downloaded from the GENCODE website (e.g. gencode.vXX.annotation.gtf.gz), I didn’t see any obvious “TSS” entry. So, how does one goes about defining “GENCODE TSS? What does this statement EVEN MEAN?? My theory: So, within…

I want to plot the EnrichedHeatmap using the GenomicRanges of my CNA data. The normalizeToMatrix function returned mat1, which is filled with 0, resulting in Error: You should have at least two distinct break values. when I try to plot it. library(EnrichedHeatmap) library(GenomicRanges) library(data.table) library(ChIPseeker) library(tibble) library(AnnotationHub) library(IlluminaHumanMethylation450kanno.ilmn12.hg19) library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb…

DOI: 10.18129/B9.bioc.crisprDesign   This is the development version of crisprDesign; for the stable release version, see crisprDesign. Comprehensive design of CRISPR gRNAs for nucleases and base editors Bioconductor version: Development (3.17) Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and…

Identification of TGFβ signaling pathway mutations in endometrial cancer We profiled the data from uterine tumors deposited to the cBioPortal of Cancer Genomics for mutations of the TGFβ signaling pathway20,21 and identified several mutations in TGFβ-related receptors (TGFBR1, TGFBR2, ACVR1B, ACVR1C, ACVR2A, ACVR2B) and transcription factors (SMAD2, SMAD3, SMAD4) (Supplementary…

This week our guests are Marit Inngjerdingen from the Institute of Clinical Medicine in Norway; Kyle Forcier, senior director of life sciences product marketing at Model N; and Dr. Andreas Roetzer, head of R&D for vaccines at Biomedical Research & Bio-Products. The next breakthrough in cancer treatment? In our body,…

Can ChiPseeker be as highly customizable as “computeMatrix”? for example if I want to plot the distribution of genes on the TAD boundary? 0 @8f91699d Last seen 21 hours ago Hong Kong It’s like “computeMatrix” in deeptools, computeMatrix scale-regions -R TAD.boundaries.bed -S gene.density.bw gives the distribution of the eigenvalues (in…

A gain-of-function screen for regulators of gene silencing We utilized the native Arabidopsis gene FWA as a reporter to screen for regulators of gene silencing. FWA encodes a transcription factor that causes a late flowering phenotype when overexpressed, resulting in a greater number of leaves produced before flowering. In Col-0…

Both high FA and low FA intake increases de novo mutation rate and disrupt genome DNA methylation in the offspring. a Violin Plot of DNSNV/DNM (de novo mutation) counts among the three different FA dietary groups (sample size for each group was as follows; combined panel: 0.3 ppm group n = 26;…

2. MicroRNA Biogenesis and Targeting MiRNAs are small non-coding single-stranded RNAs encoded within non-coding sequences of the genome; however, a minority of miRNAs are known to also be encoded within exons [3]. Interestingly, miRNAs located within intronic regions of protein-coding genes can be transcribed from the same promoter as a…

Incyte (Nasdaq: NASDAQ:) today announced that it will discontinue the Phase 3 LIMBER-304 trial following results of a pre-planned interim analysis conducted by an independent data monitoring committee (IDMC) indicating that the study is unlikely to meet the primary endpoint in the intent-to-treat patient population. The recommendation to stop the…

Overview Product name ChIP Kit (Histones, ChIP-seq) Product overview ChIP Kit (Histones, ChIP-seq) (ab270812) provides a robust ChIP protocol suitable for the investigation of histone modifications within chromatin from cells and tissues. The protocol involves protein-DNA cross-linking with formaldehyde, followed by cell…

WILMINGTON, Del., March 03, 2023–(BUSINESS WIRE)–Incyte (Nasdaq:INCY) today announced that it will discontinue the Phase 3 LIMBER-304 trial following results of a pre-planned interim analysis conducted by an independent data monitoring committee (IDMC) indicating that the study is unlikely to meet the primary endpoint in the intent-to-treat patient population. The…

I am using ChIPseeker to annotate MACS2 peaks files from publicly available data. To begin, I’m trying to first annotate the peaks the way that the authors did in the publication. This is what they say they did – “Gene annotation of the regions bound by indicated proteins were performed…

I am using ChIPseeker to annotate MACS2 peaks files from publicly available data. To begin, I’m trying to first annotate the peaks the way that the authors did in the publication. This is what they say they did – “Gene annotation of the regions bound by indicated proteins were performed…

Abstract Rivers are vital components of the biosphere and an excellent habitat for many of the Earth’s organisms. The prime focus of this study is the Iloilo River located in the City of Iloilo, Panay Island, Philippines. It is classified as Class C body of water. In spite of the…

Segmentation Segmentation algorithms partition the genome into regions with distinct epigenomic profiles. These are genomic regions of similar signal pattern over a selected number of assays. To segment the genome for each cell type we currently use either ChromHMM (Ernst et al., 2011) or Segway (Hoffman et al., 2011). These…

Harmonizing datasets for eQTL and co-regulation analysis We combined 14 eQTL datasets into the ‘MetaBrain’ resource to maximize statistical power to detect eQTLs and create a brain-specific gene co-regulation network (Fig. 2, Supplementary Figs. 1–7 and Supplementary Table 1). Previous to quality control (QC), MetaBrain includes 7,604 RNA-seq samples and…

Architecture of cyanobacterial CAST systems Starting from the known CAST components, we searched for conserved genes and genetic elements in their vicinity. These elements included the left and right ends of the transposon, the neighboring tRNA, CRISPR arrays and tracrRNA, the transposase genes (tnsB, tnsC and tniQ), and genes in…

Early detection (pancreatic cancer) cfMeDIP-seq, 5hmC sequencing LR elastic-net Hierarchical clustering, t-SNE, LR with elastic-net penalization Methylation (5mC-5hmC) 208 (72/136) 24-feature 5mC, 27-features 5hmC, 51-features combined model SML, UML Combined 5mC and 5hmC AUC of 0.997 (sensitivity 0.938, specificity 0.955) Median total reads: 17.4 M, 0.8 nonduplicate mapping rate pms.cd120.com/PDAC/index.html…

The first vaccine to potentially prevent Staphylococcal-induced toxic shock syndrome (TSS) has successfully completed a phase 2 study. TSS is a life-threatening condition caused by toxins that can lead to multiple organ failure and death. Nosocomial pathogen methicillin-resistant Staphylococcus aureus (MRSA) bacteria are resistant to widely-used antibiotics. Infections with MRSA…

CellOverview of the Oracle algorithm The CellOracle workflow is made up of several steps. We Tested and implemented CellOracle Python Versions 3.6 and 3.8 were developed and made available for use in the Jupyter Notepad environment CellOracle code can be downloaded open-source on GitHub.github.com/morris-lab/CellOracle), along with detailed descriptions of functions…

How to identify the batch informations from the sample ID? 0 I have thousands of samples from TCGA retrieved using TCGABiolinks. I want to remove the batch effect from the datasets. It’s mentioned that batch can be detected from sample ID itself How do we identify the batch info from…

DOI: 10.18129/B9.bioc.TSRchitect     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see TSRchitect. Promoter identification from large-scale TSS profiling data Bioconductor version: 3.14 In recent years, large-scale transcriptional sequence data has yielded considerable insights into the nature of gene expression and regulation in…

Comparison of read level and improving the mapping efficiency according to trimming Since the generation of high-quality WGBS data ultimately impacts the quantification and interpretation of Cs methylation levels, it is indispensable to monitor the raw data quality and interrogate the appropriate pre-processing step to cleanse data [1]. To avoid…

The bioBakery help forum Sign Up Log In Log In Popular Announcing MetaPhlAn 4MetaPhlAn Announcing HUMAnN 3.5HUMAnN Clear guidance needed for comparing across samples with varying sequencing depthMetaPhlAn List of taxa in Metaphlan4 databaseMetaPhlAn Metaphlan 4 install issueMetaPhlAn ERROR: The MetaPhlAn2 taxonomic profile provided was not generated with the database…

lncRNA expression according to breast cancer clinicopathological subtypes To identify lncRNAs expressed by specific breast cancer subtypes or associated with clinicopathological features, we analyzed RNA-sequencing data from two large independent breast cancer cohorts: SCAN-B (n = 3455)17 and TCGA-BRCA (n = 1095). We focused on lncRNAs annotated in the Ensembl18 v93 non-coding reference transcriptome…

. 2022 Jun 17;3(3):101491. doi: 10.1016/j.xpro.2022.101491. eCollection 2022 Sep 16. Affiliations Expand Affiliations 1 Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA. 2 Institute for Memory Impairments and Neurological Disorders (MIND), Irvine, CA, USA. 3 Mathematical, Computational and Systems Biology Program, UC Irvine, Irvine, CA, USA….

Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…

The clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) defensive system is an acquired mechanism in prokaryotes which is analogous to RNAi in eukaryotes [1]. The CRISPR machinery is a complex immune strategy that is continually evolving in the bacterial genome to accommodate the rapid changes in the nucleic acids of…

Transcription Start Site 2 What are the best databases to check out the transcription start sites of specific genes in human genome? TSS • 130 views wget -q -O – “http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz” | gunzip -c | awk ‘(int($7)< int($8)) {if($4==”+”) {printf(“%s\t%d\t%d\t%s\t%s\n”,$3,$7,int($7)+1,$2,$4);}else {printf(“%s\t%d\t%d\t%s\t%s\n”,$3,int($8)-3,$8,$2,$4);}}’ chr1 69090 69091 ENST00000335137.3 + chr1 139306 139309 ENST00000423372.3…

Associated RNAi Experiments Homology BLAST of peroxisomal multifunctional enzyme type 2-like vs. L. salmonis genes Match: EMLSAG00000010112 (supercontig:LSalAtl2s:LSalAtl2s668:190059:194758:1 gene:EMLSAG00000010112 transcript:EMLSAT00000010112 description:”augustus_masked-LSalAtl2s668-processed-gene-1.1″) HSP 1 Score: 102.064 bits (253), Expect = 2.195e-25Identity = 65/191 (34.03%), Postives = 101/191 (52.88%), Query Frame = 0 Query: 134 GKVALVTGAGGGLGKAYALLLASRGASVVVNDLGGSRTGEGQSSKAADEVVNEIRQKGGKAV—–GNYDSVEDGEAVIKTALDNFGRIDIVINNAGILRDRSIGRTSDSDWDLVQKVHLRGAFQVIRAAWPHMKKQKYGRIINTSSVAGIFGNFGQSNYSSAKAGLIGLTSTLAIEGERSGIQANVIVP 319 GKVAL+TGA G+G++ A+L A…

Designing the mammalian methylation array The CMAPS algorithm is designed to select a set of Illumina Infinium array probes such that for a target set of species many probes are expected to work in each species (see “Methods” section). Array probes are sequences of length 50 bp flanking a target CpG…

. 2021 Dec 31;33(6):708-718. doi: 10.21147/j.issn.1000-9604.2021.06.07. Affiliations Expand Affiliations 1 Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China. 2 Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China. 3 Department of Medical…

We are unable to reproduce the error you are seeing and we also recentlyexperienced temporary issues with our site. Please let us know if youare still having this problem. Post by Gang WeiDear manager of UCSC Genome Browser,Glad to write to you. I’m now using UCSC genome browser to check…

Significance Hairpin pyrrole-imidazole (Py-Im) polyamides can be programmed to bind a broad repertoire of DNA sequences. Py-Im small molecules can be used to target cancer-specific coding regions and block transcription elongation. This transcription blockage by Py-Im cannot be rescued by transcription elongation factors, such as TFIIS. The mechanism by which…

O304 treatment prevents islet gene expression signature changes induced by HFD We have previously demonstrated that the AMPK activator O304 improves blood glucose homeostasis in both human T2D subjects as well as in high-fat diet induced obese and diabetic mouse models. In the present study, we have now analysed the…

doi: 10.1093/nar/gkab1221. Online ahead of print. Yang Yang  1   2 , Liwei Zhang  3 , Chaoyang Xiong  2 , Jun Chen  2   4   5 , Li Wang  6 , Zengqi Wen  2   5 , Juan Yu  2 , Ping Chen  4 , Yanhui Xu  6 , Jingji Jin  1   7   8 , Yong Cai …

I am using Homer to identify peaks in RNA-seq data and then determine differential expression by counting reads per peak. Homer has a lovely package that does just this: getDifferentialPeaksReplicates.pl. The issue is that for some reason Homer returns the same peak multiple times in its final output (Bonus question:…

RPKM on TSS using DiffBind 1 Hi everyone, I want to extrapolate RPKM value from Diffbind. Investigated regions are TSS (± 2.5kb) but around 3500 TSS are “lost” because merged. I have read that in the new version of DiffBind is possible to use dbObj_region$config$mergeOverlap with negative value to avoid…

Bacterial contamination in urban areas of the main Ecuadorian rivers All rivers showed E. coli levels above standard concentrations for bathing-water recommended by the USA, European and Brazilian guidelines (Fig. 1), in concordance with other studies in Latin America, such as Colombia34, Mexico4, and Perú35. Most of the rivers in this…

Bedfile format deeptools 1 Hello everyone, Using deeptools I am trying to plot the enrichment in Genebody and TSS for this we have to give one BED file region of interest in computeMatrix. I am bit confused about the format based on a thread in biostar TSS metaprofile using Deeptoolsbased…

Why Us    Illumina are growing at pace, and we are looking for the best customer focused Bioinformatics Support Scientist to join our mission, to improve human health by unlocking the power of the genome. By joining Illumina as a Bioinformatics Support Scientist in our EMEA Head Office, Cambridge UK, you will help support…

Introduction Gene expression is not only controlled by DNA sequences but also by epigenetic marks in eukaryotes. DNA methylation as one of the important epigenetic modifications has been demonstrated as closely related to gene expression in biological processes, such as transcriptional activity, developmental regulation, and environmental responses (Maunakea et al.,…

Abstract A critical challenge for microbiology and medicine is how to cure infections by bacteria that survive antibiotic treatment by persistence or tolerance. Seeking mechanisms behind such high survival, we developed a forward-genetic method for efficient isolation of high-survival mutants in any culturable bacterial species. We found that perturbation of…

Extracting variations in the gene regions and from 100 bp of gene boundary from multiple VCF files 0 Hi, I sincerely hope that I am not repeating an already answered question. I couldn’t find the answer to my exact problem. I have three VCF files derived using bcftools (isec). Those…

computematrix how to set certain TSS 1 how to set certain TSS deeptools computematrix, I want to visualize the certain gene’s TSS up/downstream instead of whole gene,but how can I do it ? thanks. deeptools • 34 views You probably want the reference-point mode as described here. You will also…