Categories
Tag: Cutadapt
UMI workflow resulting in bams with empty reads
Hello all, In my NGS workflow for UMI based reads, I first tried identifying and removing sequence adapters using bbmerge and cutcadapt: BBMERGE -Xmx1g -ignorejunk in1=SAMPLE_R1 in2=SAMPLE_R2 outa= adapters.fa itn CUTADAPT -a forward_adapter -A reverse_adapter -o s_2_1_sequence_trimmed_UN.fastq.gz -p s_2_2_sequence_trimmed_UN.fastq.gz SAMPLE_R1 SAMPLE_R2 Then, I converted the trimmed fastq files to an…
invalid deflate data (invalid code lengths set)
I am trying to trim paired end reads using Trim-Galore. I have made sure that the files match based on the total reads processed in the output txt file from trim-galore. One of the files trimmed correctly but when I try some of the others the total written and quality…
Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout
FAO. The State of World Fisheries and Aquaculture 2022: Towards Blue Transformation (FAO, 2022). Google Scholar Hua, K. et al. The future of aquatic protein: Implications for protein sources in aquaculture diets. One Earth 3, 316–329 (2019). Article Google Scholar Hardy, R. W. Utilization of plant proteins in fish diets:…
Maternal dominance contributes to subgenome differentiation in allopolyploid fishes
Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437 (2000). Article CAS PubMed Google Scholar Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–732 (2009). Article PubMed Google Scholar Comai, L. The…
Identification of Differentially Expressed Genes in Human Colorectal Cancer Using RNASeq Data Validated on the Molecular Level with Real-Time PCR
Allam RM, Al-Abd AM, Khedr A, Sharaf OA, Nofal SM, Khalifa AE, Mosli HA, Abdel-Naim AB (2018) Fingolimod interrupts the cross talk between estrogen metabolism and sphingolipid metabolism within prostate cancer cells. Toxicol Lett 291:77–85 Article CAS PubMed Google Scholar Andrews S et al (2010) FastQC: a quality control tool…
Conserved and divergent gene regulatory programs of the mammalian neocortex
Nucleus preparation from frozen brain tissue for Chromium single-cell multiome ATAC and gene expression analysis M1 tissue was obtained from three human donors (male, aged 42, 29 and 58 years), three macaque donors (male, aged 6 (Macaca mulatta), 6 (M. mulatta) and 14 (Macaca fascicularis) years), three marmoset (Callithrix jacchus)…
A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery
Flemming, H.-C. & Wuertz, S. Bacteria and archaea on earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019). Article CAS PubMed Google Scholar Flemming, H.-C., Neu, T. R. & Wozniak, D. J. The EPS matrix: The “house of biofilm cells”. J. Bacteriol. 189, 7945–7947 (2007). Article CAS …
MetaSPAdes genome assembly (shotgun metagenome singleend) – usegalaxy.org support
Busrak December 11, 2023, 3:31pm 1 Hi friends, Metagenomic single end raw data with cut adapt‘Maximum error rate 0.3’Match times: 1Minimum overlap length:3minimum lenght: 15Max N: 0.3Max expected errors: 30 parameters.Then I aligned the host genome with gallus gallus with BBmap tool. I want to Assembly unmapped read. However, MetaSPAdes…
Resin acids play key roles in shaping microbial communities during degradation of spruce bark
Bark preparation Spruce bark was obtained from the Iggesund pulp and paper mill (Iggesund, Holmen AB, Sweden), from a bark pile resulting from stripping of spruce logs at the mill after harvest, with the average age of trees at harvest being ~70 years. The bark was left to dry at…
DNA polymerases in precise and predictable CRISPR/Cas9-mediated chromosomal rearrangements | BMC Biology
Cell culture The human endometrial carcinoma HEC-1-B cells were cultured in the modified Eagle’s medium (MEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a 5% (v/v) CO2 incubator. The human embryonic kidney HEK293T cells were cultured in the Dulbecco’s modified Eagle’s medium (DMEM) supplemented…
Opinion on miRNA pipeline
Opinion on miRNA pipeline 0 Dear colleagues, I am currently in the process of evaluating miRNA Seq data and would like to present my pipeline for your review. Given the absence of a dedicated bioinformatician in my department, particularly for this specific use case, I am eager to gather feedback…
Debian — Details of package cutadapt in trixie
Clean biological sequences from high-throughput sequencing reads Cutadapt helps with biological sequence clean tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Also, paired-end reads and even colorspace data is…
A natural product YSK-A blocks SARS-CoV-2 propagation by targeting multiple host genes
Hoareau, L. & DaSilva, E. J. Medicinal plants: A re-emerging health aid. Electron. J. Biotechnol. 2, 3–4 (1999). Google Scholar Jahan, I. & Ahmet, O. Potentials of plant-based substance to inhabit and probable cure for the COVID-19. Turk. J. Biol. 44, 228 (2020). Article CAS PubMed PubMed Central Google Scholar …
Quorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis
Centers for Disease Control and Prevention (U.S.). Antibiotic Resistance Threats in the United States, 2019. doi.org/10.15620/cdc:82532 (2019). Centers for Disease Control and Prevention. COVID-19: U.S. Impact on Antimicrobial Resistance, Special Report 2022. doi.org/10.15620/CDC:117915 (2022). Fricks-Lima, J. et al. Differences in biofilm formation and antimicrobial resistance of Pseudomonas aeruginosa isolated from…
Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment
Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article ADS CAS Google Scholar Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…
ESRP1 controls biogenesis and function of a large abundant multiexon circRNA | Nucleic Acids Research
Abstract While the majority of circRNAs are formed from infrequent back-splicing of exons from protein coding genes, some can be produced at quite high level and in a regulated manner. We describe the regulation, biogenesis and function of circDOCK1(2–27), a large, abundant circular RNA that is highly regulated during epithelial-mesenchymal…
Use of IDR after running MACS3 for ATAC-seq data
Use of IDR after running MACS3 for ATAC-seq data 0 Cross-posted from github (a little worried about the inactivity there; please let me know if this is not good practice) I am analyzing ATAC-seq data from human cells. I am planning to perform the following as part of my pipeline:…
Taxonomic and environmental distribution of bacterial amino acid auxotrophies
Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article ADS CAS PubMed Google Scholar Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….
LncRNA INHEG promotes glioma stem cell maintenance and tumorigenicity through regulating rRNA 2’-O-methylation
Ethics statement All mice procedures in this study were performed under an animal protocol approved by the Institutional Animal Care and Use Committee guidelines of Westlake University. The procedures and protocols for glioma patients were approved by the institutional review board of Beijing Tiantan Hospital. Informed consent was obtained from…
Multiple micronutrient deficiencies in early life cause multi-kingdom alterations in the gut microbiome and intrinsic antibiotic resistance genes in mice
Han, X., Ding, S., Lu, J. & Li, Y. Global, regional, and national burdens of common micronutrient deficiencies from 1990 to 2019: a secondary trend analysis based on the Global Burden of Disease 2019 study. eClinicalMedicine 44, 101299 (2022). Article PubMed PubMed Central Google Scholar Bailey, R. L., West, K….
Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient
Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA. 103, 626–631 (2006). Article ADS CAS PubMed PubMed Central Google Scholar Gao, C. & Guo, L. Progress on microbial species diversity, community assembly and functional traits. Biodivers. Sci. 30, 22429 (2022)….
A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo
Animal models All procedures involving animals were approved by the Institutional Animal Care and Use Committee (IACUC) at Washington University in St. Louis, MO. Veterinary care and housing was provided by the veterinarians and veterinary technicians of Washington University School of Medicine under Dougherty lab’s approved IACUC protocol. All protocols…
A tRNA-modifying enzyme facilitates RNase P activity in Arabidopsis nuclei
Chapeville, F. et al. On the role of soluble ribonucleic acid in coding for amino acids. Proc. Natl Acad. Sci. Usa. 48, 1086–1092 (1962). Article CAS PubMed PubMed Central Google Scholar Korostelev, A., Trakhanov, S., Laurberg, M. & Noller, H. F. Crystal structure of a 70S ribosome–tRNA complex reveals functional…
Troubleshooting cutadapt failed jobs – troubleshooting
Hoping to revive this. Same problem here. Ran Trim Galore on approx 50fastq files. 44 of them worked fine (produced output files). 3 of the paired files did not.SoSample1 R1Sample1 R2 Sample2 R1Sample2 R2 etc… did not work. The error for these say: Could not detect version of Python used…
Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls
World Health Organization. Facts sheet: suicide. www.who.int/news-room/fact-sheets/detail/suicide. National Institute of Mental Health. Suicide. www.nimh.nih.gov/health/statistics/suicide. Nock MK, Hwang I, Sampson N, Kessler RC, Angermeyer M, Beautrais A, et al. Cross-national analysis of the associations among mental disorders and suicidal behavior: findings from the WHO world mental health surveys. PLoS Med. 2009;6:e1000123….
Correction of a homoplasmic mitochondrial tRNA mutation in patient-derived iPSCs via a mitochondrial base editor
Human induced pluripotent stem cells (iPSCs) Reprogramming and Culture This study was ethically approved by the Medical Ethics Committee of Nanjing Maternal and Child Health Care Hospital (2021KY-131), and informed consents were obtained from the patient’s legal guardian as well as the healthy donors, in accordance with the Declaration of…
Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls [PeerJ]
Introduction The microbiomes of different host organisms are currently described by using culture-independent sequencing methods (Harvey & Holmes, 2022). Shotgun metagenomic and 16S rDNA sequencing methods are commonly used to identify the taxonomic composition of microbial communities in several studies (de Melo et al., 2020; Mackelprang et al., 2011; Monaco…
How to install or uninstall “cutadapt” on Linux Mint 20.3 “Una” ?
1. Install cutadapt package Please follow the steps below to install cutadapt package: sudo apt install cutadapt Copy 2. Uninstall / Remove cutadapt package This tutorial shows how to uninstall cutadapt package: sudo apt remove cutadapt Copy sudo apt autoclean && sudo apt autoremove Copy 3. Details of cutadapt package…
How to install or uninstall “cutadapt” on Ubuntu 21.10 (Impish Indri) ?
1. Install cutadapt package Please follow the guidance below to install cutadapt package: sudo apt install cutadapt Copy 2. Uninstall / Remove cutadapt package Learn how to uninstall cutadapt package: sudo apt remove cutadapt Copy sudo apt autoclean && sudo apt autoremove Copy 3. Details of cutadapt package Package: cutadapt…
how to deal with Gs?
Small RNA sequencing using Illumina 2 channel SBS: how to deal with Gs? 1 I’m working on a small RNA sequencing experiment (150 PE on NovaSeq 6000), and many reads look like this when the fragment size is smaller than 150 bp, with Gs completing the sequence up to 150:…
NGS Training | Top NGS Courses | Online Training | RNASeq | Genome Variant Detection
NGS Training Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which…
How-to: NGS Quality Control
Thanks to the introduction of high-throughput next generation sequencing (NGS) methods, generating nucleic acid sequencing data has never been easier. Now, DNA and RNA samples can be sequenced within hours, creating millions of DNA fragments (known as reads), which can then be aligned to a reference genome. Quality control is…
cutadapt ‘cut_prefix’ substring
cutadapt ‘cut_prefix’ substring 0 Dear Biostars, I’d like to add a substring of the UMI to the name of each fastq line. Below is an example of what I’d like to do (that doesn’t work) where I’d like to cut the first 7bp of R1 but only append the name…
Plugin error from cutadapt (qiime 2023.7.0) – Technical Support
Hi there! Trying to run my samples using QIIME2 2023.7. As a novice, cutadapt has never been an issue before. However, while running my samples today I encountered the following error: The command used was: qiime cutadapt trim-paired –i-demultiplexed-sequences paired-end-demux.qza –o-trimmed-sequences paired-end-trimmed.qza Where could I have gone wrong? Quick help…
Genome-wide chromatin interaction map for Trypanosoma cruzi
Johnson, P. J., Kooter, J. M. & Borst, P. Inactivation of transcription by UV irradiation of T. brucei provides evidence for a multicistronic transcription unit including a VSG gene. Cell 51, 273–281 (1987). Article CAS PubMed Google Scholar Matthews, K. R., Tschudi, C. & Ullu, E. A common pyrimidine-rich motif…
How long should the AAA… sequence be at the end of read, so that fastqc and multiqc consider it as poly- tail
How long should the AAA… sequence be at the end of read, so that fastqc and multiqc consider it as poly- tail 0 Good evening, The multiqc report shows the presence of poly- tails in my samples after DNA (!) sequencing even after cleaning with fastp and cutadapt with appropriate…
Accepted python-cutadapt 4.4-1 (source) into unstable
—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Thu, 28 Sep 2023 23:32:37 +0530 Source: python-cutadapt Architecture: source Version: 4.4-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Nilesh Patra <nil…@debian.org> Closes: 1045930 Changes: python-cutadapt (4.4-1) unstable; urgency=medium . [ Lance Lin ] * Team upload….
Methamphetamine-induced region-specific transcriptomic and epigenetic changes in the brain of male rats
Jayanthi, S., McCoy, M. T. & Cadet, J. L. Epigenetic Regulatory Dynamics in Models of Methamphetamine-Use Disorder. Genes 12, 1614 (2021). Article CAS Google Scholar Meredith, C. W., Jaffe, C., Ang-Lee, K. & Saxon, A. J. Implications of chronic methamphetamine use: a literature review. Harv. Rev. Psychiatry 13, 141–154 (2005)….
The succession of epiphytic microalgae conditions fungal community composition: how chytrids respond to blooms of dinoflagellates
Jones EBG, Suetrong S, Sakayaroj J, Bahkali AH, Abdel-Wahab MA, Boekhout T, et al. Classification of marine Ascomycota, Basidiomycota, Blastocladiomycota and Chytridiomycota. Fungal Divers. 2015;73:1–72. Article Google Scholar Van den Wyngaert S, Ganzert L, Seto K, Rojas-Jimenez K, Agha R, Berger SA, et al. Seasonality of parasitic and saprotrophic zoosporic…
Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast
Rubin, S., Parr, T., Da Costa, L. & Friston, K. Future climates: Markov blankets and active inference in the biosphere. J. R. Soc. Interface 17, 20200503 (2020). Article CAS PubMed PubMed Central Google Scholar Cantonati, M. et al. Characteristics, main impacts, and stewardship of natural and artificial freshwater environments: Consequences…
How To Read Chip-Seq Data
Source: Youtube.com The era of big data has revolutionized the way we analyze and interpret complex biological systems. In the field of genomics, Chip-Seq (Chromatin Immunoprecipitation Sequencing) data has become a valuable resource for understanding gene regulation and the functionality of the genome. Chip-Seq data provides insights into the binding…
ATAC-seq troubleshoot – Just Noise
ATAC-seq troubleshoot – Just Noise 0 Hi everyone, I have been processing paired end 150bp ATAC-seq data, but failing to get peaks at known promoters, the data just looks like noise through out. Started with QC, where reads had poly(G) towards their ends, this is known to happen in NovaSeq…
Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation
Abstract Existing monitoring approaches in heart transplantation lack the sensitivity to provide deep molecular assessments to guide management, or require endomyocardial biopsy, an invasive and blind procedure that lacks the precision to reliably obtain biopsy samples from diseased sites. This study examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) as…
High-quality single-cell transcriptomics from ovarian histological sections during folliculogenesis
Introduction Single-cell RNA sequencing (RNA-seq) was first achieved by using a quantitative cDNA amplification method and applied to mouse oocytes (Kurimoto et al, 2006; Tang et al, 2009). It has since provided unprecedented opportunities for the study of cellular differentiations, states, and diseases in various biological fields, including developmental biology,…
Remove Illumina universal adapters – Technical Support
lea.k (Lea Kauer) September 18, 2023, 7:59am 1 Hi everyone, I have reads with Barcodes in sequence and the sequencing facility told me, all the adapters are removed, but the fastqc report shows me, that they are not. Since Illumina Universal adapters and polGare detected in the forward and the…
Single-cell brain organoid screening identifies developmental defects in autism
Stem cell and cerebral organoid culture conditions Feeder-free hES cells or iPS cells were cultured on hES cell-qualified Matrigel (Corning, catalogue no. 354277)-coated plates with Essential8 stem cell medium supplemented with bovine serum albumin (BSA). H9 embryonic stem cells were obtained from WiCell. Cells were maintained in a 5% CO2 incubator at 37 °C….
if I dont know what primers in my sequencing data,How do I use qiime2 – General Discussion
cjj102664 (俊杰 陈) September 10, 2023, 3:52pm 1 Does anyone know,it is necessary to run qiime cutadapt trim-paired before run dada2. Hello @cjj102664. Welcome to the forums! cjj102664: it is necessary to run qiime cutadapt trim-paired before run dada2. Not necessarily! cutadapt will ‘cut adapters’ from your input reads. Some…
RNA-sequencing and bioinformatics analysis | COPD
Introduction COPD, a common preventable and treatable disease characterized by persistent airflow limitation and respiratory symptoms, is associated with exposure to harmful environments. COPD is currently the third leading cause of death globally. The high incidence and mortality of COPD, which seriously threaten human health, represent a public health problem…
Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes
Orr, H. A. The genetic theory of adaptation: A brief history. Nat. Rev. Genet. 6, 119–127 (2005). Article CAS PubMed Google Scholar Dillon, M. E. & Lozier, J. D. Adaptation to the abiotic environment in insects: the influence of variability on ecophysiology and evolutionary genomics. Curr. Opin. Insect Sci. 36,…
Ancient DNA reveals genetic admixture in China during tiger evolution
Johnson, W. E. et al. The late Miocene radiation of modern felidae: a genetic assessment. Science 311, 73–77 (2006). Article CAS PubMed Google Scholar Li, G., Davis, B. W., Eizirik, E. & Murphy, W. J. Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae). Genome Res. 26,…
Trimming of reads in miRNA-Seq data
Trimming of reads in miRNA-Seq data 0 Dear All, I have been trying to filter out reads from Fastq files from miRNA-Seq that we received. The read structure looks like the one shown in the figure below. I can use Cutadapt to filter out the adapter (we have the adapter…
The non-classical major histocompatibility complex II protein SLA-DM is crucial for African swine fever virus replication
Cell lines and viruses Cell lines were received from the cell culture collection for veterinary medicine (CCVM) of the Friedrich-Loeffler-Institut (FLI). The highly passaged wild boar lung cell line (WSL-R-HP, #1346; abbreviated as WSL) was maintained in Ham’s F12 cell culture medium (Ham’s F-12, 5.32 g/L; IMDM, 8.80 g/L; NaHCO3, 2.45 g/L; pH 7.2)…
In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis
Mouse models C57BL/6J (strain 000664, The Jackson Laboratory) and B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*/-EGFP)Fezh/J (strain no. 026179, The Jackson Laboratory) were used for all experimental procedures. The Npm1c/Flt3-ITD/Cas9 model has been extensively described previously31,57,58. The maximal tumor size allowed by the Home Office license for this project and authorized by the Animal Welfare Ethical…
PacBio 16S pipeline
QIIME2 analysis pipeline 0. activate conda environment conda activate qiime2-2019.10 1. flip sequences to the same direction mkdir raw_data_rc/ mkdir raw_data_cat/ parallel -j 8 ‘seqtk seq -r {} > raw_data_rc/{/.}_rc.fastq’ ::: rawdata/*.fastq parallel -j 8 –link ‘cat {1} {2} > raw_data_cat/{1/.}_cat.fastq’ ::: rawdata/*.fastq ::: raw_data_rc/*_rc.fastq 2. trim primers mkdir trimmed_reads/…
Reply to: Revisiting the intrinsic mycobiome in pancreatic cancer
Fletcher, A. A. et al. Revisiting the intrinsic mycobiome in pancreatic cancer. Nature doi.org/10.1038/s41586-023-06292-1 (2023). Aykut, B. et al. The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL. Nature 574, 264–267 (2019). Article ADS CAS PubMed PubMed Central Google Scholar Alam, A. et al. Fungal mycobiome drives IL-33 secretion…
cutadapt tool
cutadapt tool 0 Hi Members, I need to use cutadapt to trim the adapter sequences and save these adapter sequences in a fastq file along with the cutadapt output files. Is there a way to do this? Or can I use cutadapt without trimming the adapter? cutadapt • 164 views…
cutadapt in qiime2-2022.11 – Technical Support
D_S (Dharmesh Singh) July 31, 2023, 10:25am 1 sample_id.csv (575 Bytes) cutadapt_trimming.log.txt (809 Bytes) env_log.txt (3.1 KB) list_log.txt (48.3 KB) qiime_info_log.txt (782 Bytes) Hello Forum, I am running qiime2 on a virtual machine (Hyper V manager, Windows 10 professional) and I am stuck at the step where I am trying…
A genome catalogue of lake bacterial diversity and its drivers at continental scale
Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14–49 (2011). Article CAS PubMed PubMed Central Google Scholar Pernthaler, J. Competition and niche separation of pelagic bacteria in freshwater habitats….
Rewiring cancer drivers to activate apoptosis
Weinberg, R. A. The action of oncogenes in the cytoplasm and nucleus. Science 230, 770–776 (1985). Article ADS CAS PubMed Google Scholar Davoli, T. et al. Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell 155, 948–962 (2013). Article CAS PubMed PubMed Central Google Scholar Sanchez-Vega,…
Subject:[QIIME2.2023.5] Need help with Qiime2 installation: ResolvePackageNotFound error – Technical Support
Subject: Need help with Qiime2 installation: ResolvePackageNotFound error Dear Qiime2 Community, I hope this message finds you well. I am currently facing an issue during the installation of Qiime2 and would greatly appreciate your assistance in resolving it. During the installation process, after following the Qiime2 instructions, I encountered the…
With cutadapt, is it possible to completely trim reads to empty reads instead of removing them?
With cutadapt, is it possible to completely trim reads to empty reads instead of removing them? 0 I am using cutadapt to extract multiple barcode sequence elements from reads into their own fastq files as required by downstream processing. reads look like that: N(Pattern_A)(BARCODE_1)(Pattern_B)(Barcode_2)(Pattern_C)N I can first filter all the…
AAV-mediated delivery of a Sleeping Beauty transposon and an mRNA-encoded transposase for the engineering of therapeutic immune cells
Hayes, C. Cellular immunotherapies for cancer. Ir. J. Med. Sci. 190, 41–57 (2021). Article PubMed Google Scholar Laskowski, T. & Rezvani, K. Adoptive cell therapy: living drugs against cancer. J. Exp. Med. 217, e20200377 (2020). Article CAS PubMed PubMed Central Google Scholar June, C. H., O’Connor, R. S., Kawalekar, O….
Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group
Isolate storage, growth, and identification Historical BFG isolates originally cultured from clinical material between 1973 and 2018 were stored either lyophilized or frozen in skim milk media at the National Institutes of Health Clinical Center Department of Laboratory Medicine (Bethesda, MD). Isolates were de-identified and metadata including year and source/site…
Humans as blood-feeding sources in sylvatic triatomines of Chile unveiled by next-generation sequencing | Parasites & Vectors
Kent RJ. Molecular methods for arthropod bloodmeal identification and applications to ecological and vector-borne disease studies. Mol Ecol. 2009;9:4–18. doi.org/10.1111/j.1755-0998.2008.02469.x. Article CAS Google Scholar Gómez-Díaz E, Figuerola J. New perspectives in tracing vector-borne interaction networks. Trends Parasitol. 2010;26:470–6. doi.org/10.1016/j.pt.2010.06.007. Article PubMed Google Scholar Hylton A, Fitzpatrick DM, Suepaul R, Dobson…
removing overrepresented sequences from rna-seq
removing overrepresented sequences from rna-seq 1 I have a lot of rna-seq paired end data which have a very good quality, but some of the files have a lot of overrepresented sequences, not adapters. I made a blast of these sequences. Some of them didn’t match to anything, and some…
Removing overrepresented sequences in paired end RNA-seq
Removing overrepresented sequences in paired end RNA-seq 0 After trimming and QC’ing RNAseq for adapters with trim_galore, should I remove overrepresented sequences that FastQC identifies as possible adapter/primer source? If so, is there a way to do so automatically? For what it’s worth, both of the identified sequences start with…
Adapter content increases after trimming by Cutadapt
Adapter content increases after trimming by Cutadapt 0 Hi, I have utilized Cutadapt to remove adapters from my ChIP-seq data. However, when I attempted to trim one of my datasets, the adapter content actually increased from 1% to 15% after trimming. This is quite unusual as I have never encountered…
Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013). Article CAS PubMed PubMed Central Google Scholar Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013). Article CAS PubMed PubMed Central Google Scholar Zetsche, B. et al. Cpf1 is a single…
For loop in bash script
For loop in bash script 0 Hi all, I’m expecting to get 17 different paired-end fastq files (34 in total), so I want to make a bash script to just run my code through all the fastq files in a directory at once. How can I change the name of…
Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB gene
Gleckman R, Blagg N, Joubert DW. Trimethoprim: mechanisms of action, antimicrobial activity, bacterial resistance, pharmacokinetics, adverse reactions, and therapeutic indications. Pharmacother J Hum Pharmacol Drug Ther. 1981;1:14–9. Article CAS Google Scholar Amyes SG. The success of plasmid-encoded resistance genes in clinical bacteria. An examination of plasmid-mediated ampicillin and trimethoprim resistance…
adaptors removal before using bowtie for bam generation (from fastq)
adaptors removal before using bowtie for bam generation (from fastq) 1 hello, I would like to run AS analysis using rMATS from 2 reps of human rna-seq data (2 fastq files – single end), I first ran fastqc on the files and got that there are illumina universal adaptors –…
Cut site preference allows influenza A virus PA-X to discriminate between host and viral mRNAs
Gaucherand, L. & Gaglia, M. M. The role of viral RNA degrading factors in shutoff of host gene expression. Annu. Rev. Virol. 9, 213–238 (2022). Article PubMed Google Scholar Bercovich-Kinori, A. et al. A systematic view on influenza induced host shutoff. eLife 5, e18311 (2016). Article PubMed PubMed Central Google…
Dryad | Data — RNAseq data from: Medial prefrontal cortex samples of glutamate dehydrogenase-deficient mice, stress-exposed or -naive, and their Nestin-Cre+ controls
Glutamate abnormalities in the medial prefrontal cortex (mPFC) are associated with cognitive deficits. We previously showed that homozygous deletion of CNS glutamate dehydrogenase 1 (Glud1), a metabolic enzyme critical for glutamate metabolism, leads to schizophrenia-like behavioral abnormalities and increased mPFC glutamate; mice heterozygous for CNS Glud1 deletion (C-Glud1+/- mice) showed…
Y chromosome loss in cancer drives growth by evasion of adaptive immunity
Caceres, A., Jene, A., Esko, T., Perez-Jurado, L. A. & Gonzalez, J. R. Extreme downregulation of chromosome Y and cancer risk in men. J. Natl Cancer Inst. 112, 913–920 (2020). Article PubMed PubMed Central Google Scholar Kido, T. & Lau, Y. F. Roles of the Y chromosome genes in human…
Missing primers in multi amplicon sequencing
Missing primers in multi amplicon sequencing 0 Hello, I’ve received some Illumina 2x250bp data with multiple overlapping amplicons (all in the same fastq files). The fastqc report looks great and so are the gels before. What I did next was to look for the primers with cutadapt to make sure…
Installation error: undefined symbol: PyFPE_jbuf
On an up to date Centos 7 installation, I can’t do anything to make this error go away. I understand that it shouldn’t effect our ability to run the software, but the error remains. [root@slurm-01 cutadapt-1.9.1]# find . -name “*.pyc” -exec rm -rf {} \; [root@slurm-01 cutadapt-1.9.1]# [root@slurm-01 cutadapt-1.9.1]# /usr/bin/python2.7…
A dataset of micro biodiversity in benthic sediment at a global scale
Sample collection Deep-sea sediment samples were collected from the Atlantic Ocean, the Pacific Ocean and the Indian Ocean using sealable sampling boxes (Oktopus, Germany) during the 22nd, 26th, 30th, 34th, 38th, 39th, 40th and 45th cruises of Oceanic Vessel No. 1. The longitude, latitude, depth and other essential information of…
Antibiotics | Free Full-Text | Whole Genome Sequencing and Phenotypic Analysis of Antibiotic Resistance in Filifactor alocis Isolates
1. Introduction Filifactor alocis is an obligate anaerobic, non-sporeforming, Gram-positive rod [1,2]. This microorganism was first described in 1985 after being isolated from patients with periodontitis or gingivitis [3]. However, it was not until the early to mid-2000s, with the improvement of molecular identification techniques, when F. alocis was first…
IJMS | Free Full-Text | Analysis of CircRNA Expression in Peripheral Blood of Holstein Cows in Response to Heat Stress
1. Introduction With the global temperature rise, the dairy industry is confronted with a significant challenge brought about by severely damaging impacts of heat stress. Heat stress increases mortality rates and threatens the health of livestock, especially in highly productive and intolerant species. The increase in ambient temperature–humidity index (THI)…
Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017). Article CAS PubMed Google Scholar Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015). Article …
How to identify index sequences for cutadapt for atac-seq
I am just starting on my atac-seq analysis (not very experienced, so my apologies for a stupid question), and I am wanting to trim the adapters of off my paired-end reads. I am following the galaxy atac-seq protocol that says to enter in the custom 3′ adapter sequence. I took…
Efflux pump gene amplifications bypass necessity of multiple target mutations for resistance against dual-targeting antibiotic
Strains and growth conditions All strains and plasmids used in this work are described in Supplementary Table 1. The clinical isolates were obtained from the Cystic Fibrosis Foundation Isolate Core at Seattle Children’s Hospital and were originally isolated from two different cystic fibrosis patients. Distribution of these isolates is covered by…
Genome-resolved carbon processing potential of tropical peat microbiomes from an oil palm plantation
Dargie, G. C. et al. Age, extent and carbon storage of the central Congo Basin peatland complex. Nature 542, 86–90 (2017). Article ADS CAS PubMed Google Scholar Page, S. E., Rieley, J. O. & Banks, C. J. Global and regional importance of the tropical peatland carbon pool. Global Change Biology…
Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil
Study sites Soils were collected from two different sites (ARDEC: Colorado State University’s Agricultural Research, Development and Education Center in Fort Collins, CO; and CPCRC: USDA Columbia Plateau Conservation Research Center in Pendleton, OR). At each site, four replicate plots of no-till corn (ARDEC) or no-till annual wheat (CPCRC) were…
acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens
acCRISPR framework acCRISPR performs essential gene identification by calculating two scores for each sgRNA, namely the cutting score (CS) and the fitness score (FS). CS and FS are the log2-fold change of sgRNA abundance in the appropriate treatment sample with respect to that in the corresponding control sample (see Supplementary…
ChatGPT optimized for bioinformatics questions
Tool:ChatGPT optimized for bioinformatics questions 1 Hey everyone! I launched a new chatbot today that is bioinformatics focused! It’s trained on bioinformatics content and should help debug / ideate much faster for you than vanilla ChatGPT. Check it out here: ai.tinybio.cloud/chat Thanks! gpt • 165 views • link updated 1…
Correct way to remove Nextera adapters from ITS sequences
Correct way to remove Nextera adapters from ITS sequences 0 Hi everyone, I think this question has been coming up a few times but it didn’t help me solve my issue. I have FastQ files from ITS amplicon based metagenomic sequencing (ITS1/2) (300 bp) and FastQC tells me that they…
Characterization of nuclear DNA diversity in an individual Leymus chinensis
Introduction The definition of an individual organism, traditionally defined by the invariable presence of a physiological unit and genetic homogeneity, is challenged by situations such as intraorganismal genetic heterogeneity (IGH), which refers to the presence of more than one genotype in a single organism (Schweinsberg et al., 2015). Cells within a…
EvE Premium
Upgrade In Progress: EvE Premium is unavailable during the upgrade process. The new, upgraded version is scheduled for release in May 2023. Create Your Own Bioinformatics Pipeline: Powerful and Easy-to-use. Design your own ultra-fast, cloud-based pipeline in seconds. Use defaults or define specific parameters. It’s your choice! Preprocessing ✯ Alignment & Mapping…
Curated and harmonized gut microbiome 16S rRNA amplicon data from dietary fiber intervention studies in humans
Carlson, J. L., Erickson, J. M., Lloyd, B. B. & Slavin, J. L. Health effects and sources of prebiotic dietary fiber. Curr. Dev. Nutr. 2, nzy005 (2018). Article PubMed PubMed Central Google Scholar Deehan, E. C. et al. Precision microbiome modulation with discrete dietary fiber structures directs short-chain fatty acid…
Analysis of tRNA-derived small RNAs
Introduction Sarcoidosis is a multisystem inflammatory disease of unknown aetiology that is characterised by non-caseating epithelioid granulomatous lesions (aggregates of lymphocytes, macrophages, epithelioid cells, and giant cells).1 Typical clinical features include bilateral hilar lymph node lesions, pulmonary infiltration, and eye and skin lesions. Some patients may also have neurological and…
The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation
Hunt, T. et al. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318, 1913–1916 (2007). Article ADS CAS PubMed Google Scholar Crowson, R. A. The phylogeny of coleoptera. Annu. Rev. Entomol. 5, 111–134 (1960). Article Google Scholar Darwin, C. The Descent of Man, and Selection…
Circulating miRNA expression in long-standing type 1 diabetes mellitus
Participants This is an observational case–control study, carried out in adult patients who attended the Endocrinology and Nutrition Service of the Central University Hospital of Asturias, between June 2019 and December 2021. Written informed consent was obtained from all participants and the study was conducted in accordance with the principles…
Error while running Megahit
Error while running Megahit 0 Hi, Myself Abhirami, Currently pursuing Ph.D., for a paper publication currently I’m working on mitogenomic sequences. So as the initial steps, I proceed successfully with fastp (Quality checking), cutadapt, bwa mem (to remove host genome). But, while running megahit, I reached up with many difficulties…
qiime cutadapt demux failed to exclude reads with fake barcodes in the middle – Technical Support
Below is my command.qiime cutadapt demux-paired –i-seqs asap2_out/imported/fqMuBiPe-1.qza –m-forward-barcodes-file input//fqMuBiPe-1/metadata.tsv –m-forward-barcodes-column barcode-sequence –o-per-sample-sequences asap2_out/demultiplexed/fqMuBiPe-1-demux.qza –o-untrimmed-sequences asap2_out/demultiplexed/fqMuBiPe-1-untrimmed.qza The output has many partial reads because there were reads (e.g. reverse complementary, or contaminants) with no barcode at the beginning, but with a fake barcode (randomly matched) in the middle, and qiime mistook…
Cutadapt error: too many parameters.
Cutadapt error: too many parameters. 0 Hi biostars community! I am having issues to loop cutadapt over gunzipped samples. This is the script I am using: #!/bin/bash #SBATCH –account GRINFISH #SBATCH -c 8 #SBATCH –mem 96g #SBATCH –output logfile.out #SBATCH –error logfile.err # This script performs trimming for PE sequences…
Assigned taxonomy after dada2 only “NAs” or “Mitochondria”
Hi, I followed the dada2 tutorial on 16S and ITS amplicon metagenomic data from soil samples. However, when trying to assign a taxonomic rank to my ASV table using DECIPHER, I only get “NAs”. When using the dada2 native’s Bayesian method, I get “NA” or “Mitochondria” (family). For my 16S…
Diversity and compositional differences of the airborne microbiome in a biophilic indoor environment
Klepeis, N. E. et al. The National Human Activity Pattern Survey (NHAPS): A resource for assessing exposure to environmental pollutants. J. Expo. Anal. Environ. Epidemiol. 11, 231–252 (2001). CAS PubMed Google Scholar Richardson, A. et al. Office design and health: A systematic review. N. Z. Med. J. 130, 39–49 (2017)….
How to write/use qiime2 script for LSF (bsub) + docker set up? – Technical Support
Hello all, I’m looking for guidance on how to write a non-interactive job script for qiime2. The HPC I have access to uses LSF and docker images, which are both new to me. So far, I have been creating an interactive shell to use qiime2 (I created a .sh file…
The effects of host quantitative genetic architecture on the gut microbiota composition of Chinook salmon (Oncorhynchus tshawytscha)
Anderson MJ (2001) A new method for non‐parametric multivariate analysis of variance. Austral Ecol 26(1):32–46 Google Scholar Anderson MJ (2004) PERMDISP: a FORTRAN computer program for permutational analysis of multivariate dispersions (for any two-factor ANOVA design) using permutation tests. Department of Statistics, University of Auckland, New Zealand, 24. Aykanat T,…