Tag: nf-core

Detection of DNA methylation signatures through the lens of genomic imprinting

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…

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downstream analysis on the output of nf-core/rnaseq pipeline

downstream analysis on the output of nf-core/rnaseq pipeline 1 Hello everyone, I ran nf-core/rnaseq pipeline successfully, now I want to do downstream analysis like machine learning on the generated output files from this pipeline. Should I use salmon.merged.gene_counts.tsv for that and apply log transformation to normalize it before doing downstream…

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DEseq2 input

DEseq2 input 1 Hello Guys, @Michael Love I have a transcriptomics dataset and did rnaseq/nf-core pipeline by salmon-star. my output of the salmon-star folder is as follows: salmon.merged.gene_counts.tsv salmon.merged.gene_counts_length_scaled.tsv salmon.merged.gene_counts_scaled.tsv salmon.merged.gene_lengths.tsv salmon.merged.gene_tpm.tsv salmon.merged.transcript_counts.tsv salmon.merged.transcript_lengths.tsv salmon.merged.transcript_tpm.tsv tx2gene.tsv my question is: which one of these files should be an input for Deseq2…

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MAJOR Computational Biology Research Lab

MAJOR Computational Biology Research Lab (MCBRL) uses computer science algorithms to solve biology related problems, bioinformatics software development and develop bioinformatics cloud computing platforms or services for handling and analyzing large-scale biological data.. The workflow of hdWGCNA analysis for Single-cell Spatial Transcriptomics data RNA-seq Schematicsc/nRNA-seq Schematic ” RNA-seq Schematic 空间转录共表达网络分析流程…

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Nextflow bwa-mem2 pipeline/channel question

Hello, I’m trying to write a simple bwa script for my research, but it keeps failing. I have two questions in this post. The first code can be executed, but only the first paired fastq files are processed. Google search tells me it’s because the index_ch is a queue channel…

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couldn’t find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function ‘seqinfo’ for signature ‘”SummarizedExperiment”‘

Dear Michael, I have not been able to run tximeta properly. I have read #38 but could not get any clue. The quant.sf files were generated by the latest nf-core RNA-seq pipeline (3.12.0), as the pipeline did not save the Salmon index, I generated it myself. Salmon used by nf-core…

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MICA: a multi-omics method to predict gene regulatory networks in early human embryos

Introduction After the fusion of the oocyte and sperm, the zygote undergoes a series of cell divisions until it forms a blastocyst before implantation into the uterus. A human blastocyst is formed of a fluid-filled cavity and ∼200 cells that comprise three distinct cell types: the trophectoderm (TE), which gives…

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Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility

Abstract Shotgun metagenomes is a repository of all the genes present in an environmental sample. With recent advancements in bioinformatic techniques, it is now possible to in-silico retrieve sequences that belong to specific taxa, followed by assembly and annotation and the obtained sequences are called as metagenome-assembled genome (MAG), which…

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Bioinformatics Research Specialist | EmployDiversity

Med-Pediatrics – Pennsylvania-Pittsburgh – (23007857) Organizes and facilitates data collection and conducts statistical analysis of datasets while working across multiple, simultaneous projects. Applies scientific methodology and statistical analyses to implement appropriate methodologies for complex data management and statistical analyses. Facilitates algorithm development, software development, and result interpretation. Assists with grant…

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Insight Global hiring Bioinformatics Engineer in New York, NY

Job Title: Bioinformatics Engineer Company: Memorial Sloan Kettering Cancer Center – Transformational Research Team within the Center for Molecular Oncology Duration: 12-month – contract Location: Hybrid onsite 2 days a week in NYC at 321 E 61st Street Pay Rate: $62-65 (flexible) Must-haves 5-7 years of experience as a Bioinformatics…

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Will DESeq2 be appropriate tool for analysis?

Will DESeq2 be appropriate tool for analysis? 0 @959b4cc0 Last seen 12 hours ago Sweden Hello! We are looking at extra cellular RNA which has been collected from cell culture media. We used UMIs to tag and sequence nucleotides which were present in the media, processed them with nf-core RNA-seq…

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A new bioinformatics pipeline solves a 50-year-old blood group puzzle

Analysis pipeline of four GATA1 ChIP-seq datasets on primary erythroblasts. Raw sequencing data were extracted from publicly available databases (n = 4) and subjected to the above analysis pipeline adapted from nf-core for ChIP-seq analysis. Functions for each analysis step are shown next to the corresponding arrows along with the software/packages used…

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Number of accessible regions included by DESeq2 to generate the PCA plot with the nf-core ATACseq pipeline ?

Number of accessible regions included by DESeq2 to generate the PCA plot with the nf-core ATACseq pipeline ? 2 Hello everyone, I launched an analysis of some ATACseq data across different conditions. I launch the cf-core ATACseq pipeline v 1.2.1: nf-co.re/atacseq/2.1.2/docs/output In the output I have a PCA generated by…

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sarek: Introduction

Introduction nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses. The pipeline is built using…

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BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data | BMC Bioinformatics

Overview In the first alignment module, FASTQ files are checked with FastQC 0.11.8 [15], and by default samples that fail the “Adapter Content” metric are trimmed using Trim Galore! 0.6.6 [16] (see Methods: Configuration for alternative trimming options). The resulting FASTQ files are aligned to a reference genome using the…

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Change mounted drive on GCP Batch nextflow process

I’ve been trying to download and index databases to add to a GCP bucket that I will use as a database to be queried through the fusion file system using nextflow. However, I keep getting errors with the download process. Here is the filesystem of the process: Filesystem Type Size…

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scrnaseq: Introduction

Introduction nf-core/scrnaseq is a bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data. This is a community effort in building a pipeline capable to support: Alevin-Fry + AlevinQC STARSolo Kallisto + BUStools Cellranger UniverSC Documentation The nf-core/scrnaseq pipeline comes with documentation about the pipeline usage, parameters and output….

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broadinstitute – GTF To Use With Broad Institute Fasta In STAR

If you are looking for a genome and its corresponding annotations, you can use the following, it is from nf-core (link to the original doc): #!/bin/bash VERSION=108 wget -L ftp.ensembl.org/pub/release-$VERSION/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz wget -L ftp.ensembl.org/pub/release-$VERSION/gtf/homo_sapiens/Homo_sapiens.GRCh38.$VERSION.gtf.gz BTW the most up-to-date version as of today is 109. Read more here: Source link

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Error executing nf-core/metaboigniter pipeline

Error executing nf-core/metaboigniter pipeline 0 I ran this command: export NXF_VER=22.10.8; nextflow run nf-core/metaboigniter -profile test The error obtained: Error executing process > ‘get_software_versions’ Caused by: Process `get_software_versions` terminated with an error exit status (127) Command executed: echo 1.0.1 > v_pipeline.txt echo 22.10.8 > v_nextflow.txt Rscript -e “cat(as.character(packageVersion(‘CAMERA’)),’\n’)” &> v_camera.txt…

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Sarek did not perform variant calling?

I’m trying to check for mutations from whole exome sequencing of two samples from the same patient, and was recommended to use the nextflow sarek pipeline. I assembled the fastq files I needed, made the csv file describing the patient sample information (patient, sample, lane, fastq_1, fastq_2), and entered the…

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Help to get differential_peaks.bed to use for findMotifsGenome.pl?

Help to get differential_peaks.bed to use for findMotifsGenome.pl? 0 Hi all, I am trying to use the command findMotifsGenome.pl from HOMER that needs differential_peaks.bed file as input. I used nf-core/atac-seq then DiffBind but not sure how to get differential_peaks.bed file. Would you please have a suggestion? Do I need to…

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DEseq2 input from nf-core/rnaseq

DEseq2 input from nf-core/rnaseq 1 I used the nf-core/rnaseq pipeline in the cluster human genome, and I got some files as the output of Star salmon. My question is which file I use as input to DESeq2? and where is the full file that contains 58,000 genes? salmon.merged.gene_counts_length.tsv (29744 genes)…

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Heatmap for ATAC-seq

Heatmap for ATAC-seq 0 Hi all, I apply similar code that I used for RNA-seq (DeSeq2) to ATAC-seq to make a heatmap, so I am not use if it still makes sense. The function here is Heatmap(), not pheatmap(). Instead of count matrix for genes, here I use consensus_peaks.mLb.clN.featureCounts.txt, a…

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Desq2 input from nf-core/rnaseq

Desq2 input from nf-core/rnaseq 0 I used the nf-core/rnaseq pipeline in the cluster human genome, and I got some files as the output of Star salmon. My question is which file I use as input to DESeq2? and where is the full file that contains 58,000 genes? salmon.merged.gene_counts_length.tsv (29744 genes)…

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nf-core/sarek

Introduction Sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses. It’s built using Nextflow, a…

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nf-core/marsseq

Introduction nf-core/marsseq is a bioinformatics single-cell preprocessing pipeline for MARS-seq v2.0 experiments. MARS-seq is a plate-based technique that can be combined with FACS in order to study rare populations of cells. On top of the pre-existing pipeline, we have developed an RNA velocity workflow that can be used to study…

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nf-core/gwas

Introduction This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline. The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to…

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nf-core/circdna

nf-core/circdna is a bioinformatics analysis pipeline for the identification of circular DNAs in eukaryotic cells. The pipeline is able to process WGS, ATAC-seq data or Circle-Seq data to give insights into the circular DNA landscape in your samples. In total, the user can choose between 5 different branches inside the…

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nf-core/configs

abims The ABiMS cluster profile slurm adcra CRA HPC profile slurm alice Profile for use on Academic Leiden Interdisciplinary Cluster Environment (ALICE). slurm aws_tower AWS Batch with Tower Profile awsbatch awsbatch AWSBATCH Cloud Profile awsbatch azurebatch Azure BATCH Cloud Profile azurebatch azurebatchdev Azure BATCH Dev Cloud Profile azurebatch bi Boehringer…

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Renders a collection of sequences into a pangenome graph.

nf-core/pangenome is a bioinformatics best-practice analysis pipeline for pangenome graph construction. The pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics,…

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Registration open for Nextflow Summit 2023, and free online Nextflow / nf-core training

News:Registration open for Nextflow Summit 2023, and free online Nextflow / nf-core training 0 Hi all! We have a bunch of Nextflow events coming up after the summer! First up, registration for the 2023 Nextflow Summit events is LIVE! We had lots of requests for an event in the US,…

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Efficient parallel taxonomic profiling for metagenomics with nf-core/taxprofiler

James Fellows Yates, Moritz E. Beber, Sofia Stamouli, Lauri Mesilaakso, Tanja Normark, Jiang Ou, Thomas A. Christensen II, Maxime Borry Taxonomic profiling addresses the challenge of genetically identifying all possible taxa that may be present in a metagenomic sample. However, different algorithms, parameters, and reference databases often yield different results….

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Replicate

Replicate 1 I’m doing RNA-seq with the nf-core pipeline and have the following worries about the samples: I have 9 biopsy for one patient after treatment. So, should I treat the 9 samples as a technical replicate, a biological replicate, or an independent sample? Replicate • 33 views If these…

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nf-core/marsseq: systematic pre-processing pipeline for MARS-seq experiments

Abstract As a result of advancing single sequencing technology (scRNA-seq), it has become possible to study gene regulatory mechanism(s) and their influence on evolving cell states in time at the level of individual cells. Since 2009, numerous scRNA-seq protocols have been developed, each with its own advantages, disadvantages and library…

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systematic pre-processing pipeline for MARS-seq experiments

%PDF-1.4 % 93 0 obj <> endobj 113 0 obj <>stream application/pdf Martin Proks nf-core/marsseq: systematic pre-processing pipeline for MARS-seq experiments 2023-06-08T07:43:26Z Word 2023-06-30T02:12:09-07:00 2023-06-30T02:12:09-07:00 macOS Version 13.4 (Build 22F66) Quartz PDFContext uuid:98ec5752-1dd1-11b2-0a00-8a0827bd7700 uuid:98ec575e-1dd1-11b2-0a00-900000000000 endstream endobj 5 0 obj <> endobj 2 0 obj <> endobj 90 0 obj <> endobj…

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Can’t find a variant which suppose must have in a vcf file

Can’t find a variant which suppose must have in a vcf file 0 Hi all, I get a vcf file after running nf-core pipeline then I annotated ID column using bcftools. But when I search for a variant which know must have because the sample from a person has this…

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nf-core/rnaseq pipeline

nf-core/rnaseq pipeline 0 Hi all, I use the nf-core/rnaseq pipeline in the cluster, which results in the following error: Error: r2-scr unexpectedly ended before r1-src caused by: unexpected end of file. rnaseq pipeline nf-core • 44 views • link updated 1 hour ago by Ram 39k • written 2 hours…

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How to get genes associated with open chromatin regions?

How to get genes associated with open chromatin regions? 1 Hi all, I ran ATAC-seq pipeline such as nf-core and got output files such as bam, bigwig, broadpeak. Would you suggest a way to get genes associated with open chromatin regions? I used ChIPpeakAnno but for DiffBind. Thank you so…

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Convert Bam to Fastq

Convert Bam to Fastq 0 Hi All, Using this command line, I converted two Paired bam files: samtools fastq -1 ${sampleID}.sorted_1.fastq -2 ${sampleID}.sorted_2.fastq ${sampleID}.sorted.bam 1st File: Bam 8.4G Fastq1 8.1G and fastq2 8.1G were produced. Fastq1 494M and fastq2 494M were made by Bam 1.8G. Then I use the nf-core…

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“nextflow pull nf-core/sarek –help” returned “connection failed” ?

“nextflow pull nf-core/sarek –help” returned “connection failed” ? 2 Hi, I am trying to use nextflow and an nf-core pipeline for the first time. I have installed nextflow and nf-core and tried to run this simple command but got the “connection failed” error. I got the same error for a…

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Bioconductor Unevensamplesizes

Answer: multiple filters in biomaRt by RuBBiT0 &utrif; 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…

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Yersinia pestis genomes reveal plague in Britain 4000 years ago

All radiocarbon dates were calibrated in OxCal 4.4 using the IntCal20 calibration curve18,19. There is no stable carbon and nitrogen isotopic evidence for any detectable input of marine or freshwater foods that would require a correction for reservoir effects. Charterhouse Warren: Archaeological context Charterhouse Warren is a natural shaft in…

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Docker Error while running nf-core/rnaseq pipeline

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…

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Sr. Bioinformatics Engineer II Job Opening in Cambridge, MA at ModernaTX, Inc.

Job Description: The Role In this role, you will develop bioinformatics pipelines and implement the latest algorithms. You will work closely with computational biologists, statisticians, bioinformaticians, and scientists within Oncology and software engineers in our Digital organization to develop our next-generation bioinformatics pipelines. Here’s What You’ll Do Develop, test, and…

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Amazon Omics Beefs up Managed Services with Pre-Built Workflows, GPU Support

BOSTON – Amazon Web Services this week introduced new features for its nascent Amazon Omics service, including a collection of “pre-built” workflows, support for graphical processing units (GPUs), direct data uploads through an application programming interface (API), and streamlined variant querying and analysis. AWS launched Amazon Omics last November. The…

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Help with Diffbind result

Help with Diffbind result 0 @3fdb6f97 Last seen 8 hours ago United States Hi all, I am trying to find which genes are different in chromatin accessibility so I used nf-core/ATAC pipeline then feed the bam files and broadpeak files output into Diffbind. I got around 100k peaks, 21k genes…

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Error while running nf-core/rnaseq pipeline

Error while running nf-core/rnaseq pipeline 1 Hello guys! I am trying to run the nf-core/rnaseq pipeline with the following parameters: nextflow run nf-core/rnaseq -r 3.10.1 –input samplesheet.csv –outdir output –fasta chr22_with_ERCC92.fa -profile docker –gtf chr22_with_ERCC92.gtf –max_memory 200GB I keep getting a persistent error: WARN: Got an interrupted exception while taking…

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Singularity image is not working in nextflow

Singularity image is not working in nextflow 0 Hello everyone, I’m having trouble getting Singularity to work with my custom bcftools pipeline in Nextflow. I’ve tested my pipeline with Conda and it works great. However, when I install software locally (instead of using Conda), it runs approximately 10 times faster…

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The little skate genome and the evolutionary emergence of wing-like fins

Nakamura, T. et al. Molecular mechanisms underlying the exceptional adaptations of batoid fins. Proc. Natl Acad. Sci. USA 112, 15940–15945 (2015). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Turner, N. et al. The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids. Proc. Biol. Sci….

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Announcing the 3rd round of the Nextflow and nf-core mentorship

🚨APPLICATIONS FOR THE NF-CORE AND NEXTFLOW MENTORSHIP ARE NOW OPEN!🚨 Thanks to funding from the Chan Zuckerberg Initiative, the third round of the Nextflow and nf-core mentorship program is now open 🤗 If you’re looking to get into the world of workflows, have a look! 👉 nf-co.re/mentorships Mentors + mentees…

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Nextflow rnaseq finishing early

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…

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nf-core/isoseq: Simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing

doi: 10.1093/bioinformatics/btad150. Online ahead of print. Affiliations Expand Affiliations 1 The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG. 2 Wobble Genomics, University of Edinburgh, Edinburgh, EH25 9RG. Item in Clipboard Sébastien Guizard et al. Bioinformatics. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/bioinformatics/btad150. Online ahead…

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Nextflow memory issues custom config -c

Nextflow memory issues custom config -c 1 Hi all, I am trying to run nextflow on my laptop nextflow run nf-core/rnaseq \ –input samplesheet.csv \ –genome mm10 \ -profile docker I am having issues with memory: Error executing process > ‘NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (KO_3)’ Caused by: Process requirement exceed available memory –…

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docker – Permissions error running NextFlow RNAseq test pipeline

I’ve been trying to run a minimal example of the NextFlow RNAseq pipeline, like so: nextflow run nf-core/rnaseq -r 3.10.0 -profile test,docker –outdir /home/kai/RNASeq/rnaseq_test/test_output However, this appears to return the error below: Error executing process > ‘NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)’ Caused by: Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)` terminated with an error exit status (1)…

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Command line training – genotoul-bioinfo

  The GenoToul bioinformatics platform, Sigenae and SaAB (MIAT) offers a catalog of training sessions. If you need bio-informatic training on tools which are not covered in the existing catalog please feel free to contact us (please add “Request for training” in the subject of your demand). For example we have…

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Virtual Nextflow and nf-core training event in 5 languages

News:March 13-16: Virtual Nextflow and nf-core training event in 5 languages 0 Have you ever wanted to learn how to author and use data analysis pipelines? Next to Snakemake, Nextflow has certainly been the fastest growing DSL for authoring bioinformatic data analytics pipelines in the past years, but of course…

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Which input file is used for DGEList in EgdeR?

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…

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Bioinformatics Technical Analyst at University of Colorado Anschutz Medical Campus in aurora, Colorado

Job Description: Bioinformatics Technical Analyst – 28519 University Staff Description University of Colorado Anschutz Medical Campus Department: Office of Information Technology Job Title: Bioinformatics Technical Analyst Position: #00804692 &ndash; Requisition: #28519 Job Summary: The Bioinformatics Technical Analyst will assist biological sciences researchers in making effective use of a High-Performance Computing…

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nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs | BMC Bioinformatics

Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci. 1976;73(11):3852–6. doi.org/10.1073/pnas.73.11.3852. Article  CAS  Google Scholar  Arnberg AC, Van Ommen G-JB, Grivell LA, Van Bruggen EFJ, Borst P. Some yeast mitochondrial RNAs…

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Extracting list of target genes from ChIP-seq bigwig file

Extracting list of target genes from ChIP-seq bigwig file 1 I am reading a publication where the authors performed ChIP-seq on a specific TF. Their data was deposited on NCBI in bigwig format. I would like to extract the final list of target genes. Is this possible using the bigwig…

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Tools/pipeline for analysis of smart-seq3 data

Tools/pipeline for analysis of smart-seq3 data 1 I have Smart-Seq3 data and zUMIs refuses to work. Is there any other alternative? Nf-core pipelines rnaseq and scrnaseq doesn’t support sm3 yet. I am also prepared to go down the manual route. Has anyone tried umi_tools or alevin at least to demultiplex…

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pipeline launch from nf-core website

pipeline launch from nf-core website – input csv bug · Issue #811 · nf-core/sarek · GitHub Labels bug Something isn’t working You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window….

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nf-core presentation – HackMD

<!– .slide: data-background=”raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg&#8221; –> <a href=”nf-co.re”><img src=”raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-darkbg.svg&#8221; width=”60%”></img></a> # What is nf-core\? [Maxime U Garcia](https://maxulysse.github.io/) ▸ [<i class=”fa fa-twitter” aria-hidden=”true”></i>@gau](https://twitter.com/gau/) | [<i class=”fa fa-github” aria-hidden=”true”></i>@maxulysse](https://github.com/maxulysse/) [Karolinska Institutet](https://ki.se/) | [Science for Life Laboratory](https://www.scilifelab.se/) Sweden — ## Overview – 🗄️ [Barntumörbanken](https://ki.se/forskning/barntumorbanken/) – 🧬 [NGI](https://ngisweden.scilifelab.se/) – 🍬 [Nextflow](https://www.nextflow.io/) – 🧙 [nf-core](https://nf-co.re/) — ##…

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Implement tests with pytest-workflow – githubhot

Pytest workflow makes it easier to maintain larger test suites and also allows to check outputs. cf. github.com/nf-core/tools/issues/605, github.com/nf-core/rnaseq/pull/546, github.com/nf-core/sarek/tree/dev/tests Testing scenarios: Run pipeline with more than one file different parameter combinations different filenames and folder structures for cellranger run subworkflows with and without index different protocols, if we manage…

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Mapped reference id is not an id of the genome file genome_nowhitespace.fa

miRDeep2: Mapped reference id is not an id of the genome file genome_nowhitespace.fa 1 Hi everyone, I’m trying to run nf-co.re/smrnaseq pipeline and I’m having a problem with mirdeep2. Command: nextflow run nf-core/smrnaseq -profile ijcluster –input /home/794_both.fastq.gz –outdir /home/results –genome GRCh38 –protocol qiaseq –mature mirbase.org/ftp/CURRENT/mature.fa.gz –hairpin mirbase.org/ftp/CURRENT/hairpin.fa.gz Error message: Command…

Continue Reading Mapped reference id is not an id of the genome file genome_nowhitespace.fa

bam – Detect mutation context in a read of a sam file

That kind of custom fiddling with reads and variants is very cumbersome, non-standard and also error-prone. Do a standard variant callign pipeline and then filter for the mutations that you want. Then extract the variant position (so the coordinates) and get the variant context from the reference genome. Using individual…

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Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples?

Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples? 0 Hi, I have some shotgun metagenomics gonorrhea samples and I want to use metagenomics pipeline to process the samples and then detect antimicrobial resistance. I looked into few pipelines so far for metagenomics data such as…

Continue Reading Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples?

How to pass custom software specific variables to nf-core/sarek nextflow pipeline?

How to pass custom software specific variables to nf-core/sarek nextflow pipeline? 0 I’m attempting to call whole genome variants using nf-core/sarek nextflow pipeline. In QC step there is an option that invokes trim_galore quality trimming, but i don’t know how to pass my custom adapters to be cut as well….

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