PPT-The FASTQ format and quality control

Author : roy | Published Date : 2024-01-13

Bioinformatics and functional genomics IMB Bioinformatics Group November 02 2017 A G C T 1 Cluster identification by local maxima of intensity values 2 Background

Presentation Embed Code

Download Presentation

Download Presentation The PPT/PDF document "The FASTQ format and quality control" is the property of its rightful owner. Permission is granted to download and print the materials on this website for personal, non-commercial use only, and to display it on your personal computer provided you do not modify the materials and that you retain all copyright notices contained in the materials. By downloading content from our website, you accept the terms of this agreement.

The FASTQ format and quality control: Transcript

Bioinformatics and functional genomics IMB Bioinformatics Group November 02 2017 A G C T 1 Cluster identification by local maxima of intensity values 2 Background subtraction noise removal. Bioinformatics Workshop:. File Formats for Next Gen Sequence Analysis. Gigabases. Cost per Kb. Lucinda Fulton, The Genome Center at Washington University. Cost. Throughput. Sequencing Technologies. http://www.geospiza.com/finchtalk/uploaded_images/plates-and-slides-718301.png. FASTQ-to-FASTA. FASTQ/A Clipper. FASTQ/A . Collapser. Bowtie. PARalyzer. FMR.clusters. = “binding sites”. (note there are other . PARalyzer. output). # . Collapse redundant reads to speed up . alignment (can also use . Galaxy overview and Interface. Getting Data in Galaxy. Analyzing Data in Galaxy . Quality Control. Mapping Data. History and workflow. Galaxy Exercises . (https://. galaxy.bioinfo.ucr.edu. /). NGS Analysis Using Galaxy. John . Derber. NCEP/EMC. Reference slide at end. Quality Control - General. Quality control in data assimilation is used to ensure that the analysis is not degraded by the inclusion of certain observations. &. Recruiter Trainings. Cye. Fink. About. Quality Control. Incorporated in the 2008 Rules and . Regs. . . Each state must produce 70% of its COEs from the previous year. . There are 7 state requirements for quality control.. NGS/. MPS. Precourse. . materials. Yonglan Zheng. (yzheng3@uchicago.edu). 2017.6.10. Precourse. . materials. General NGS variant calling workflow . [slide#3. ]. GATK . Best Practice as an . example. Retrieving sequence data files. and. L. inux commands. Nov 17, 2016. Joe Troy. Agenda. Schedule meetings for upcoming sessions. Retrieving Sequence files (.. tgz. ) from the . biotec. server. Demonstration. File formats are often ignored by users. Applications automatically save files in the application’s format. All formats are made for a reason, efficiency, effectiveness – saving the information needed to recreate the document as saved. for Insect Rearing. 2017. Norm Leppla. University of Florida. Entomology and Nematology. Department. . . Norm’s Career in Insect Rearing. University of Arizona- Insect rearing research, 2 years (pink bollworm, . Quality Assessment of Sequences. Why does quality assessment matter?. DNA -> Data = lots of processes. . => Errors can be introduced. Poor understanding of the data . => Poor Assembly. GettingStarted 1Install32Supporteddatabases73Paired-endsequencing-97%OTU94Denoising(Illuminaonly)155Single-endsequencing176AnintroductiontothedownstreamanalysiswithRandphyloseq217Computebasicstatistic Thu27-Fri28September2018UNSW,Sydney Contents1Generalinformation21.1Workshoptrainers..........................................21.2Acknowledgements..........................................31.3Learningo RT-PCR direct from blood! Your advantages Enjoy the convenient handling Efficient and flexible – set up any combination of tests with the liquid test mix and the same PCR program for different 2. nd. August 2019. Sequencing history. Current sequencing approaches. File formats. Quality assessment. Read trimming. DAG workflows. The Sequence Read Archive. Outline. Descriptive text. Example commands – black monospaced text: .

Download Document

Here is the link to download the presentation.
"The FASTQ format and quality control"The content belongs to its owner. You may download and print it for personal use, without modification, and keep all copyright notices. By downloading, you agree to these terms.