Tag: nf-core
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…
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…
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…
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…
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…
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….
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…
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…
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…
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 –…
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)…
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…
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…
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…
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 – Requisition: #28519 Job Summary: The Bioinformatics Technical Analyst will assist biological sciences researchers in making effective use of a High-Performance Computing…
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…
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…
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…
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….
nf-core presentation – HackMD
<!– .slide: data-background=”raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg” –> <a href=”nf-co.re”><img src=”raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-darkbg.svg” 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/) — ##…
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…
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…
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…
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…
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….
