Tag: bcl2fastq

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

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

Participant selection and sample collection Informed consent was obtained for five adult volunteers. The study protocols were reviewed and approved by the Advarra Institutional Review Board (Advarra, Inc., Columbia, MD). All analyses were performed according to the relevant guidelines and regulations. Fecal collection was completed by self-sampling, which has proven…

Tissue collection and crypt isolation A small piece of colon is collected from individuals who have undergone surgery to remove part of the colon under the standard of care at either Keck Hospital of USC or Children’s Hospital Los Angeles through the Norris Comprehensive Cancer Center Translational Pathology Core. A…

Ethical approval, DNA samples and oligonucleotides All patients provided written informed consent to allow the collection of blood and/or tumor tissue and the analysis of clinical and genetic data for research purposes. The IRB of the Dana-Farber Cancer Institute and New York University Grossman School of Medicine approved these protocols….

Introduction The metabolome is an incredibly diverse collection of small molecules (<1,500 Da) in biological systems involved in virtually every cellular process, including cellular energy production, macromolecule synthesis, epigenetic modifications, cell signalling and more (for recent reviews see [Citation1–6]). It responds rapidly (in seconds) to both internal (signalling, allostery) and external…

NGS demultiplexing 1 Hello everyone, I am working on a linkage project for Sars COV-2. I used Illumina iseq1000 for sequencing. The indexes I use for the study are designed as 10bp, but they were entered as 8bp during the operation of the device. When I demultiplex with bcl2fastq, all…

bcl2fastq error with RunInfo.xml 0 Dear all, I am running to an error with bcl2fastq. I have slightly different setup – I have received ONLY two files from the sequencing company in order to run conversion. One of the files is in tar.gz.dm5 which contains a single line: daac12b61f03f01d303f7b47f9118994 220202_VH00203_129_AAANKJFM5.tar.gz…

Tool Tool Name Description Removes adapter sequences and trims low quality bases from the 3′ end of reads. Overlapping paired-ended reads can be merged into consensus sequences and adapter sequence can be found for paired-ended data if not known. Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data….

To maximize reproducibility, a list of the reagents and resources used in this study, as well as their source and identifier, is provided in Supplementary Table 5. Experimental model and subject details Oral swab samples were obtained from bottlenose dolphins (Tursiops truncatus) managed by the U.S. Navy MMP Biosciences Division, Space…

Introduction Cholangiocarcinoma (CC) is a form of gastrointestinal cancer that originates from the epithelium of either intrahepatic or extrahepatic bile ducts. It accounts for approximately 3% of all gastrointestinal cancers, with reported incidence of one to two cases per 100,000 persons per year in the USA (and much higher incidence…

Ethics statement In vitro and animal work were conducted under appropriate biosafety conditions in a BSL-3 facility at the Institut für Virologie, Freie Universität Berlin, Germany. All animal experiments were performed in compliance with relevant institutional, national and international guidelines for the care and humane use of animals and approved…

Hi all, I have data from a single-end run with a dual index structure generated by the NextSeq 500 instrument. I want to do the demultiplexing by bcl2fastq tool. How should my SampleSheet.csv structure and bcl2fastq script look like? I used aSampleSheet structure (shared below) with a bcl2fastq command (mentioned…

Cell culture Human lung adenocarcinoma cells A549 expressing human ACE2 (A549-ACE2, NR-53821) were acquired from BEI Resources. They were maintained in DMEM/F-12 (1:1, Corning) medium supplemented with 10% FBS (GeneDepot) and blasticidin (100 μM). Normal A549 cells were purchased from ATCC (CCL-185) and cultured in DMEM/F-12 (1:1, Corning) supplemented with 10%…

Hi all, I have data from a single-end run with a dual index structure generated by the NextSeq 500 instrument. I want to do the demultiplexing by bcl2fastq tool. How should my SampleSheet.csv structure and bcl2fastq script look like? I used aSampleSheet structure (shared below) with a bcl2fastq command (mentioned…

Case selection In this prospective case‒control study, we enrolled PD patients and healthy controls at Asan Medical Center (AMC), Seoul, South Korea, between 2018 and 2020. PD diagnosis was based on the UK PD Society Brain Bank criteria15. Batch 1 (n = 210) and 2 (n = 100) PD cohorts were recruited from January…

cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11 0 Hi all, I’m attempting to use cellranger-arc mkfastq to convert BCL files to FASTQ files, but encountered with errors and would like help from you. Command I ran is: cellranger-arc mkfastq –id=ATAC1_fastq \ > –run=/mnt/c/Users/helen/Desktop/Analysis/Raw_bcl_files/ATAC1/230120_NB551308_0209_AH5W5LBGXN \ > –csv=/mnt/c/Users/helen/Desktop/Analysis/230120_NB551308_0209_AH5W5LBGXN.csv \ >…

Ethics statement Informed consent for diagnostic and research-based studies was obtained for all subjects in accordance with the Declaration of Helsinki protocols and approved by local institutional review boards (Yorkshire & The Humber – Leeds Bradford Research Ethics Committee (13/YH/0310), the Sydney Children’s Hospitals Network Human Research Ethics Committee (HREC/10/CHW/113)…

bcl2fastq on Mac 1 Does bcl2fastq work on a mac? bcl2fastq is available as a Linux rpm file bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm. I tried extracting the the rpm contents by first installing rpm2cpio on mac using brew brew install rpm2cpio seen here (macappstore.org/rpm2cpio/). Then extracted contents using rpm2cpio.pl bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm | cpio -idmv This…

Sample preparation We ordered the GIAB samples from the Coriell Institute (NA24385, NIST ID HG002; NA24149, NIST-ID HG003 and NA24143, NIST-ID HG004). DNA concentration was measured by Qubit. The library was constructed according to Illumina TruSeq DNA PCR Free Library Prep protocol HT (Illumina Inc., San Diego, CA, USA) for…

Cell isolation, reprogramming and culture Approval was obtained for human cell and tissue sample collection and genetic reprogramming from the Institutional Review Board (protocols 19–252, 18–243, 21–060, 19–284 and 415-E/1776/4-2014, Ethics Committee of the province of Salzburg). Adult samples were collected in accordance with the Declaration of Helsinki after written…

BCL compression 2 Hi, I’m trying to store some RUNs generated by different Illumina sequencers. My idea is to compress them to keep all files together (and reduce size, but this is secondary)… however, because the big amount of files and because the global size can be enormous (~120GB!) I’m…

How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger) 0 Hello all. I am trying to pre-process some single cell RNA and ADT (Totalseq-C) data from an GEO SRA, but having some issues getting separate fastq’s for the “CITE-seq” (ADT)…

DRAGEN .bcl conversion error due to improper custom p5 oligos 0 I am working on a custom library preparation method and I designed my p5 oligos incorrectly. To be specific, I used the reverse complement of the correct p5 index sequence. As a result my fastq files aren’t demultiplexing properly….

Biological materials RAW264.7, 293T and HeLa cells were obtained from ATCC. RAW264.7 cells with Tnf-mCherry reporter and relA-GFP fusion protein (RAW-G9 clone) were kindly provided by I.D.C. Fraser (National Institutes of Health). The IBA cell line derived from the stromal vascular fraction of interscapular brown adipose tissue of young male…

BBMap/BBTools reformat.sh : real error or spurious message? [W::bgzf_read_block] EOF marker is absent reformat.sh 1 When subsampling paired-end .fastq.gz files using reformat.sh from BBMap/BBTools, I get this error message: [W::bgzf_read_block] EOF marker is absent reformat.sh I’ve checked the input files with gunzip -t, no error. The input files are a…

Introduction Primary testicular diffuse large B-cell lymphoma (PT-DLBCL) is a rare and aggressive form of mature B-cell lymphoma.1–3 PT-DLBCL was the most common type of testicular tumor in men aged over 60 and characterized by painless uni- or bilateral testicular masses with infrequent constitutional symptoms.4–6 PT-DLBCL shows significant extranodal tropism,…

Study approval was provided by the Research Ethics Committee of the University of Perugia (report n.2018-21 of 11/12/2018) according to Italian Ministry of Health legislation18. All methods were carried out following relevant guidelines and regulations and the study was carried out in compliance with the ARRIVE guidelines. Informed consent is…

Hello everybody, I have a question quite different about similar topic addressed on: Post not found I tried Paul’s bash script in the web indicated above (fastq_lane_merging.sh) adapting to my filename organization data being: #!/bin/bash for i in $(find ./ -type f -name “*.fastq.gz” | while read F; do basename…

empty fastq files created by docker bcl2fastq2 v2.20 OSX 0 HI, I installed a following docker image, REPOSITORY TAG IMAGE ID CREATED SIZE zymoresearch/bcl2fastq latest 037f216c2523 13 months ago 117MB and run a following command; docker run -d –name bcl2fastq -v /Volumes/Aura2/bcl_NU/170720_NB501488_0132_AH5V32BGX3:/mnt/run -v /Volumes/Aura2/output:/mnt/out zymoresearch/bcl2fastq:2.20 -R /mnt/run -o /mnt/out/Data/Intensities/BaseCalls/Alignment_1 –barcode-mismatches…

Illumina summary.csv file units 1 We are using illumina Novaseq machines to do some sequencing and one of the files produced is a summary.csv file that has some info about the run that was sequenced. However, it is tough to figure out what units were used for a lot of…

I usually remove Ns from the sample sheet and then run this command $ bcl2fastq -i Runfolder/Data/Intensities/BaseCalls -R Runfolder -o output_directory –sample-sheet Runfolder/SampleSheet.csv -r number_of_threads -p number_of_threads -w number_of_threads –no-lane-splitting –mask-short-adapter-reads 0 –use-bases-mask Y*,I8Y9,I8,Y* Original sample sheet: Sample_ID,Sample_Name,Description,index,I7_Index_ID,index2,I5_Index_ID,Sample_Project Sample1,Sample1,,TACCGAGGNNNNNNNNN,TACCGAGGNNNNNNNNN,AGTTCAGG,AGTTCAGG,BRCA1 Sample2,Sample1,,CGTTAGAANNNNNNNNN,CGTTAGAANNNNNNNNN,GACCTGAA,GACCTGAA,BRCA1 Formatted sample sheet: Sample_ID,Sample_Name,Description,index,I7_Index_ID,index2,I5_Index_ID,Sample_Project Sample1,Sample1,,TACCGAGG,TACCGAGG,AGTTCAGG,AGTTCAGG,BRCA1 Sample2,Sample1,,CGTTAGAA,CGTTAGAA,GACCTGAA,GACCTGAA,BRCA1 Our RunInfo.xml file looks…

BCL files conversion to FASTQ without SampleSheet.csv 1 Dear community, I have got NGS data which is basically the BaseCalls folder with .bcl files. I want to know how to successfully convert .bcl files to .fastq format. So far, I have been using the bcl2fastq program, however, I have no…

Our lab has been using bcl2fastq v2.20.0.422 to demultiplex RNA-seq data sequenced on an Illumina Novaseq machine on a beefy EC2 instance and we’ve run into the strange problem: namely that while demultiplexing is very fast, generating the stats files are unbearably slow. In a recent example, we demultiplexed one…

Forum:Troubleshooting Tips – bcl2fastq creates duplicate reads 1 Hi, I have seen a few times where bcl2fastq (v2.20) will produce duplicate FASTQ entries in sequencing read IDs, raw sequences, & quality scores. This causes issues with downstreams tools like Picard MarkDuplicates (e.g. Exception in thread “main” htsjdk.samtools.SAMException: Value was put…

Get failed reads on Novaseq 0 Dear all, on a NextSeq550, I can get failed reads (not PF) with –with-failed-reads using bcl2fastq. With the more modern bclconvert software, this does not exist. support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html Also, it seems failed reads are not saved any more by the Novaseq, which is problematic for…

How to fasterq-dump 10x genomics snATACseq fastq from SRA 2 I am trying to retrieve fastq files from a 10x genomics snATACseq dataset on SRA. Each run should have 4 fastq files associated with it: I1: Dual index i7 read (optional) R1: Read 1 R2: Dual index i5 read R3:…

bcl2fastq ERROR 1 Hi all, I have a problem. I’m running bcl2fastq software on Ubuntu, but I can’t demultiplex anything as the software gives me this error: *ERROR: bcl2fastq::common::Exception: 2021-Sep-02 12:12:34: Success (0): /home/Software/bcl2fastq/src/cxx/lib/layout/Layout.cpp(693): Throw in function void bcl2fastq::layout::handleDefaultSample(bool, bool, size_t, bcl2fastq::layout::LaneInfo&, bool&) Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::InputDataError> std::exception::what: Missing a…