Tag: ChiPseq

DOI: 10.18129/B9.bioc.iASeq     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see iASeq. iASeq: integrating multiple sequencing datasets for detecting allele-specific events Bioconductor version: 3.13 It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and…

Answer: multiple filters in biomaRt by RuBBiT0 ▴ 10 First, yes, one gene could be related to several GO ID, and the result is based on the annotation package you use. Second, could you pro… Comment: Diffbind “No genome detected” by kyliecode • 0 Hi Dr. Stark, Thanks very…

DOI: 10.18129/B9.bioc.karyoploteR     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see karyoploteR. Plot customizable linear genomes displaying arbitrary data Bioconductor version: 3.13 karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them….

Junior Bioinformatics Analyst Job ID: req3312Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc.  The lab addresses some…

Hi , I’m trying to do analysis of chipseq data . I have 3 samples Sample1 , sample2 and input I have done QC and then alignment using Bowtie . After that I used samtool to get bam files . Then I have used Picard for duplicate removal. Now I…

Which data should I select in Encode chip-seq data? 1 I want to analyze the ENCODE ChIP-seq data. In this case, which data should I select? I will analyze the peaks from replicate 1 and 2 and detect the common peaks. Should I download the files ‘ENCFF162ADN’ (replicate 1) and…

CUT&Tag data processing: peak caller choice and typical peak size profile 1 Greetings everyone, I am currently analysing CUT&Tag data (a recent technique, variant of the ChIP-seq), capturing different histone variants. To do so, I tried all the different suggested tools for peaks calling: the more general MACS2 (broad peaks,…

Bioinformatics Analyst IV Job ID: req2734Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

Bioinformatics Analyst II/III Job ID: req3427Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

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:…

This is the development version of GenomicRanges; for the stable release version, see GenomicRanges. The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing…

Bioinformatics Analyst IV Job ID: req2734Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

DOI: 10.18129/B9.bioc.EDDA     This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see EDDA. Experimental…

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Infrastructure for Biostrings-based genome data packages Bioconductor version: 2.5 Infrastructure shared by all the Biostrings-based genome data packages Author: Herve Pages Maintainer: H. Pages <hpages at fhcrc.org> To install this package, start R and enter: source(“http://bioconductor.org/biocLite.R”) biocLite(“BSgenome”) To cite this package in a publication, start R and enter: citation(“BSgenome”) Documentation…

Hello, I am have ChIPseq data from histone marks from 2 different condition (mock and treated with 2 biological replicas each) and the aim of my analysis is to study whether a particular histone mark is enriched in one condition versus the other. I am new to bioinformatic and I…

ChIPseq w/ polyploid genome : Xenopus laevis 0 Hello, I have recently undertaken reanalyzing a transcription factor ChIPseq done in Xenopus laevis. I started with the raw data, which includes two replicates for a transcription factor chip, and a DNA input control file. These are all fastq files. After aligning…

samtools idxstats not removing ChrM 2 I am trying to remove ChrM from my ChIP-seq data. Below is my pipeline for one sample up to where I am having the issue (samtools idxstats). The output file from samtools idxstats is the same size as the input so it doesn’t look…

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Bioinformatics Analyst II/III Job ID: req3427Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research,…

Cell culture hTERT-RPE-1 WT and hTERT RPE-1 TP53−/− (46, XX)27 cells were a gift from J. Korbel. The cells were grown in DMEM/F-12, GlutaMAX (10565018) supplemented with 10% FBS (Thermo Fisher Scientific, 10270106) and 1% antibiotic–antimycotic (Thermo Fisher Scientific, 15240062). CP-A (KR-42421) (47, XY) cells were purchased from the American Type…

Chiseq files for deseq2 0 Hello everyone, I have 4 peaks bed files and i want to create count matrix for analysis in deseq2 I want to see the difference acetylation between them, I want in the column the 4 samples, and in the rows peaks I understand i can…

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see NarrowPeaks. Analysis of Variation in ChIP-seq using Functional PCA Statistics Bioconductor version: 2.13 The double aim of the package is to apply a functional version of principal component analysis (FPCA) to: (1) Process…

How to annotate a MACS2 peak output file that is in tabular format? 0 I am fairly new to ChIP-seq analysis. I am using data from someone else and they only have the MACS2 peak file in tabular format. I have annotated peaks previously using MACS2 .bed files using ChIPseeker,…

Infrastructure for manipulating intervals on sequences Bioconductor version: 2.6 The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially, as well as views on these sequences. Efficient list-like classes are also provided…

Hi, I am running the HTSeqGenie on both MacOS and Linux with the test TP53 samples. They both gave me error in reading the fastq files. It seems having problems reading the fastq.gz files in each parallel process. Could anyone help me with this please? Error are at below: checkConfig.R/checkConfig.template:…

Bioinformatics Analyst IV Job ID: req3398Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research,…

I am trying to index my reference genome using bwa-mem2 (latest version). I downloaded GRCm39.primary_assembly.genome.fa from www.gencodegenes.org/mouse/release_M27.html and run the following bwa-mem2-2.0pre2_x64-linux/bwa-mem2 index /media/jay/Data/reference_genome/GRCm39.primary_assembly.genome.fa I got this output [bwa_index] Pack FASTA… 7.03 sec init ticks = 216871092051 ref seq len = 5456444902 binary seq ticks = 176853625961 build index ticks…

Suppose I’m looking at a GEO entry like so: www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM946533 Notice at the bottom is a table of ‘Supplementary files’, containing broadpeak and bigwig files. I’m wondering how to download these using Entrez. I’ve tried a variety of approaches, the “closest” I’ve gotten is the following: esearch -db gds -query…

Chip-seq Analysis 0 Hi everyone, I am analyzing chipseq data and I am trying to figure out the handling of biological replicates and the best tools to use. I tried to dig into the former questions, but it is hard to navigate thorough so many information. I have 2 different…

DOI: 10.18129/B9.bioc.MIRA     Methylation-Based Inference of Regulatory Activity Bioconductor version: Release (3.15) DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and…

DOI: 10.18129/B9.bioc.gcapc     GC Aware Peak Caller Bioconductor version: Release (3.13) Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation. Author: Mingxiang Teng and…

DOI: 10.18129/B9.bioc.metaseqR2     An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms Bioconductor version: Release (3.11) Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining…

DOI: 10.18129/B9.bioc.DiffBind     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DiffBind. Differential Binding Analysis of ChIP-Seq Peak Data Bioconductor version: 3.15 Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions….

Choose the correct answer: 1. Which method should you use to identify novel targets of a selected RNA binding protein (Select all that apply). A. ChIPseq B. ATACseq C. CLIP 2. Mark all the alternative splicing events (Select all that apply). A. exon skipping B. alternative polyadenylation C. alternative promoter…

DOI: 10.18129/B9.bioc.samExploreR     This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see samExploreR. samExploreR…

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    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see MEDIPS. DNA IP-seq data analysis Bioconductor version: 3.2 MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of…

Unknown chromosome results in .narrowPeak files 1 I’ve run macs2 callpeaks and in the .narrowPeak file I have many rows for chromosomes with names like “chrUn_KI270522v1”. Can anyone tell me what this means? The peak was found in an unknown chromosome? Is this due to noise and can be ignored?…

Junior Bioinformatics Analyst Job ID: req3312Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research,…

Visualizing Chip Peak files from ENCODE 1 Hello. I am trying to view chip peak files in the WashU genome browser from Encode. Specifically I am needing to visualize the peak files for the following: ENCFF017XLW, ENCFF188SZS, and ENCFF367KIF These files are in BED format and I have found a…

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ChIPSeq Co-Localization 0 Hello, Does anyone have any tips on how to do co-localization analyses on a handful of transcription factors? I see how to do everything up to peak-calling, but after that i’m not sure how I would go ahead analyzing co-localization. Thanks! Co-localization ChIPseq • 21 views Login…

Split merged Bam file without replacement 0 Hi guys, I have 5 bam (ChIPseq PE data sorted by position) files that came from 5 different murine cortexes (mice that belong to the same group, so biological replicates), however I have a lot of group variability. I’m thinking to merge all…

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see Rsubread. Rsubread: high-performance read alignment, quantification and mutation discovery Bioconductor version: 2.13 This R package provides easy-to-use tools for analyzing next-gen sequencing read data. Functions of these tools include quality assessment, read alignment,…

ChIPseq annotation with replicates 0 Hi, What’s the best way to annotate chip peaks in case of replicates? I have 3 replicates each group. I understand Chipseeker is a very convenient tool, but I can’t find a clear example of how to merge replicates and annotate the peaks for visualization?…

Significance The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the…

DOI: 10.18129/B9.bioc.derfinder     This is the development version of derfinder; for the stable release version, see derfinder. Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach Bioconductor version: Development (3.15) This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two…

Name Last modified Size Description Parent Directory   –   Pc.consensus_peaks.annotatePeaks.txt 30-Mar-2021 19:12 1.6M   Pc.consensus_peaks.bed 30-Mar-2021 19:12 376K   Pc.consensus_peaks.boolean.annotatePeaks.txt 30-Mar-2021 19:12 2.4M   Pc.consensus_peaks.boolean.intersect.plot.pdf 30-Mar-2021 19:12 5.5K   Pc.consensus_peaks.boolean.intersect.txt 30-Mar-2021 19:12 91   Pc.consensus_peaks.boolean.txt 30-Mar-2021 19:12 1.2M   Pc.consensus_peaks.featureCounts.txt 30-Mar-2021 19:12 464K   Pc.consensus_peaks.featureCounts.txt.summary 30-Mar-2021 19:12 458  …

    This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see ChIPQC. Quality metrics for ChIPseq data Bioconductor version: 3.1 Quality metrics for ChIPseq data Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark Maintainer: Tom Carroll <tc.infomatics at gmail.com>, Rory Stark <rory.stark…

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ChIP-Seq density plot between two groups of genes 1 Hello I have Chipseq data(.bam file) from this I have normalized my bam file BPM method and created the density plot using deeptools, density plot i have created for two group of genes (Genes of interest) group of genes are different…

Chipseq density plot between two grops of genes 1 Hello I have Chipseq data(.bam file) from this I have normalized my bam file BPM method and created the density plot using deeptools, density plot i have created for two group of genes (Genes of interest) group of genes are different…

Removing contamination with SNP tools 0 Hello everyone, Currently, I’m working on a ChIPseq dataset where I will analyze chromatin marks on transposons and genes in a fungus. Unfortunately, I got some contamination in my data from a closely related species. Because they are so similar, removing contamination based on…

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see csaw. ChIP-seq analysis with windows Bioconductor version: 3.2 Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control. Author: Aaron Lun <alun at wehi.edu.au>,…

DOI: 10.18129/B9.bioc.ALDEx2     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ALDEx2. Analysis Of Differential Abundance Taking Sample Variation Into Account Bioconductor version: 3.9 A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard…

difference between treat_pileup and bdgcmp fold enrichment tracks macs2 0 Hello, I created bigwig file from a treat_pileup.bdg file generated by macs2 and also used treat_pileup.bdg and control_lambda.bdg with macs2 bdgcmp. Here is my codes; macs2 callpeak -t sample.bam -c sample_input.bam -g hs -f BAM -q 0.001 –bdg –outdir /folder…

not primary alignment flag filtering does not work 1 Hello, I have a bowtie2 result looking like this; 27823422 reads; of these: 27823422 (100.00%) were unpaired; of these: 2464773 (8.86%) aligned 0 times 19083986 (68.59%) aligned exactly 1 time 6274663 (22.55%) aligned >1 times 91.14% overall alignment rate I am…

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ChIPComp. Quantitative comparison of multiple ChIP-seq datasets Bioconductor version: 3.4 ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control. Author: Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang Maintainer:…

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    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see chipseq. chipseq: A package for analyzing chipseq data Bioconductor version: 3.4 Tools for helping process short read data for chipseq experiments Author: Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao Maintainer: Bioconductor Package…

dba.count reduces binding matrix, why? 0 db <- dba(samplesheet) This gives me: db 9 Samples, 138044 sites in matrix (193226 total) then I do db.cnt <- dba.count(db) db.cnt 9 Samples, 55893 sites in matrix I wonder why dba.count is removing more than half of the intervals? diffbind atacseq chipseq diffbind3…

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MotIV. Motif Identification and Validation Bioconductor version: 3.4 This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize…

ChIP-seq peak number so high 0 Hello everyone, I want to ask a general question and your valuable comments about my approach. I am analyzing different ChIP-seq samples from different datasets under same conditions (i.e. : mcf7 er alpha control chip-seq under the same conditions). Some of them have really…

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DOI: 10.18129/B9.bioc.systemPipeRdata     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see systemPipeRdata. systemPipeRdata: NGS workflow templates and sample data Bioconductor version: 3.9 systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used…

# this should do it, concatenate peak locations in all peaks, sort them and merge cat A B C …. | sort -k1,1 -k2,2n | mergeBed -i stdin > locations.bed To know which files the peaks co-ordinates are merged from, you need to have an identifier in each file before…

Bowtie2 alignment error with different amount of reads in R1 and R2 0 Hi all, I have an issue when trying to align a ChIPseq input reads to the genome using bowtie2. The error that comes up is: Error, fewer reads in file specified with -2 Error, fewer reads in…

How to proceed with multiple runs ChIP-seq 0 Hello dear people, I want to ask a question about multiple runs. I want to use this sample; Foxa1 ChIP-seq but it has (also the input) multiple runs: 3 runs I am not sure if I merge them and analyze them as…

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DOI: 10.18129/B9.bioc.marr     Maximum rank reproducibility Bioconductor version: Release (3.13) marr (Maximum Rank Reproducibility) is a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data. In this R package, we implement functions that measures the reproducibility of features per sample pair and sample…

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DOI: 10.18129/B9.bioc.PICS     Probabilistic inference of ChIP-seq Bioconductor version: Release (3.5) Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach. Author: Xuekui Zhang <xzhang at stat.ubc.ca>, Raphael Gottardo <rgottard at fhcrc.org> Maintainer: Renan Sauteraud <rsautera at fhcrc.org> Citation (from within R, enter citation(“PICS”)): Installation To install this…

DOI: 10.18129/B9.bioc.DESeq2     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: 3.10 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on…

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Chipseq visualization how to draw the figure 1 Dose anybody know how to draw the figure using Chpseq data？ Any guidance would be appreciated ！ (the figure is from The Histone Lysine Demethylase JMJD3/KDM6B Is Recruited to p53 Bound Promoters and Enhancer Elements in a p53 Dependent Manner) peaks Chipseq…