Tag: qualimap

Institue for Health Metrics and Evaluation. Global Burden of Disease. vizhub.healthdata.org/gbd-results/ 2019. Troeger, C. E. et al. Quantifying risks and interventions that have affected the burden of diarrhoea among children younger than 5 years: an analysis of the Global Burden of Disease Study 2017. Lancet Infect. Dis. 20, 37–59 (2020)….

That solves the problem! It is a panel data so I thought it would be expected not to have regions outside the given intervals. Maybe just for completeness, what are the implications of not supplying a –feature-file ?  Otherwise, the problem is resolved: “` QualiMap v.2.2.2-devBuilt on 2019-11-11 14:05 Selected…

Rapaka, R. R. et al. Conserved natural IgM antibodies mediate innate and adaptive immunity against the opportunistic fungus Pneumocystis murina. J. Exp. Med. 207, 2907–2919 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  Boehm, T., Iwanami, N. & Hess, I. Evolution of the immune system in the lower vertebrates. Annu….

Hajdinjak, M. et al. Initial upper palaeolithic humans in europe had recent neanderthal ancestry. Nature 592, 253–257 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Slimak, L. et al. Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France. Sci. Adv. 8, eabj9496 (2022). Article  CAS  PubMed  PubMed…

High amount of intronic/intergenic reads in SMARTer stranded total bulk RNAseq 0 Hello, I have bulk RNAseq data (SMARTer, stranded total RNA with ribo depletion, 100M paired-end reads 150bp) of 12 human samples and the QC stats look like this High mapping rate against the genome (~90% with Hisat2/STAR) Low…

Read Counts from BAM file 0 for a set of samples, paired end nextseq illumina p2 was performed. in all, i am getting read count much higher than my actual flow cell capacity. How is it even possible? my flow cell can generate total reads upto one billion (paired-end), and…

Klepzig KD, Adams AS, Handelsman J, Raffa KF. Symbioses: a key driver of insect physiological processes, ecological interactions, evolutionary diversification, and impacts on humans. Environ Entomol. 2009;38:67–77. CAS  PubMed  Google Scholar  Dale C, Moran NA. Molecular interactions between bacterial symbionts and their hosts. Cell. 2006;126:453–65. CAS  PubMed  Google Scholar  Salem…

Clarification on Sequence Duplication Levels and Qualimap Estimated Duplication Rate 0 Hello, I’m working with illumina paired-end reads. I have merged the data of 2 different runs of the same sample, in order to increase coverage depth. Firstly, I removed duplicates using picard MarkDuplicates: java -jar picard.jar MarkDuplicates \ INPUT=input.bam…

Are there pipelines to analyze the Quality Controls for ATAC-seq and ChIP-seq data? 0 Hello: Are there pipelines to analyze all of the Quality Controls for ATAC-seq and ChIP-seq data in cistrome db? cistrome.org/db/#/ I know fastqc to analyze the sequence quality, qualimap bamqc to analysis the mapping quality, are…

Sorrells RB (1974) Synovioanalysis (“liquid biopsy”). J Ark Med Soc 71(1):59 CAS  PubMed  Google Scholar  Siena S, Sartore-Bianchi A, Garcia-Carbonero R, Karthaus M, Smith D, Tabernero J, Van Cutsem E, Guan X, Boedigheimer M, Ang A, Twomey B, Bach BA, Jung AS, Bardelli A (2018) Dynamic molecular analysis and clinical…

Hello all, I recently discovered the tools bamqc and qualimap, which seem to be extremely useful. However, I have been trying to do the following call qualimap multi-bamqc -d bam-files-list.txt -outfile ../bam/reports/report.pdf -outformat PDF -r Notice that my intention is to have bamqc run before producing a multi-samples comparison (flag…

Callaway, E. Oldest Homo sapiens fossil claim rewrites our species’ history. Nature. doi.org/10.1038/NATURE.2017.22114 (2017). Article  PubMed  Google Scholar  Lucas-Sánchez, M., Serradell, J. M. & Comas, D. Population history of North Africa based on modern and ancient genomes. Hum. Mol. Genet. 30(R1), R17–R23. doi.org/10.1093/HMG/DDAA261 (2021). Article  PubMed  Google Scholar  Scerri, E….

Allikmets, R. et al. A photoreceptor cell-specific ATP-binding transporter gene (ABCR) is mutated in recessive Stargardt macular dystrophy. Nat. Genet. 15, 236–246 (1997). Article  CAS  PubMed  Google Scholar  Tanna, P., Strauss, R. W., Fujinami, K. & Michaelides, M. Stargardt disease: Clinical features, molecular genetics, animal models and therapeutic options. Br….

Back to Bioinformatics Main Menu Evaluation FastQC GCATemplates available: grace terra module spider FastQC After running FastQC via the command line, you can ssh to an HPRC cluster enabling X11 forwarding by using the -X option and view the images using the eog tool. From your desktop: ssh -X username@grace.hprc.tamu.edu From your FastQC working…

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…

Pangenome: Gene presence and absence analysis 1 Hello. I would like to have an idea for gene presence and absence determination for pangenome analysis. I have built a pangenome from several yeast strains of interest by merging each CDS and eliminate the redundantly using CD-HIT. Then, I mapped Illumina reads…

Containers are a technology for packaging and deploying software applications in a portable and isolated environment. They allow developers to bundle their application and its dependencies together in a single package, called a container. This package can then be run on any machine that has a container runtime, such as…

Low exonic mapping of RNASeq data to draft genome. Should I suspect poor annotation? 0 I am working on RNASeq data for DE from a non-traditional organism (Artemia franciscana, a eukaryotic arthropod) whose draft genome was published last year. I should note here that although the genome was assembled with…

is BBMap/Qualimap affected by log4j vulnerability 2 no, unless the tools are used as a library in a web server. It’s worth noting picard.jar and abra.jar are affected (even though as Pierre L says, these are unlikely to be attacked on most systems). If you’re responsible for systems, esp web…

Dear @Mario_Garcia,The tool should work, I tested it right now with some test data. Please make sure: (a) your data was correctly analyzed by QualiMap BAM QC (i.e., the files should not be empty),(b) your files come from the same organism and data library(c) and you data has no weird…

qualimap2 mean mapping quality 0 I’ve done a contrast experiment to see the difference between the bam with BQSR and the bam without BQSR. I use qualimap to evaluate both bams. This is the confusing part. Using hap.py and the giab na12878 truth vcf, shows the bam with BQSR is…

Introduction Thyroid tumors are the most common malignant tumors of the endocrine system, and their incidence has been increasing in the recent decades. Currently, there are some target drugs that can effectively treat PTC, and next-generation sequencing (NGS) can be used for targeted therapy. In order to make better informed…