(517) 353 0368

  • Github
  • Twitter
  • Linkedin
  • Research Gate

mansfeld@msu.edu

  • Home

  • My Research

  • Publications

  • Software

  • Blog

  • More

    Reproducing Yang et al. - Chr1 Joint Genotyping

    March 9, 2017

    Reproducing Yang et al - HaplotypeCaller

    March 8, 2017

    Reproducing Yang et al - BQSR

    March 6, 2017

    Please reload

    Archive

    March 2017

    February 2017

    December 2016

    November 2016

    October 2016

    May 2016

    Please reload

    Tags

    AddOrReplaceReadGroups

    Aspera

    BAM

    BQSR

    BWA

    Bootstrapping

    ENA

    FASTX

    FastAlternativeReferenceMaker

    FastQC

    GATK

    GenotypeGVCF

    HaplotypeCaller

    INDELs

    Joint Genotyping

    Nipponbare

    Picard

    PicardTools

    QTLseq

    Read Groups

    SNPs

    SRA

    SelectVariants

    Sequencing

    Trimmomatic

    VariantFiltration

    automation

    bioinformatics

    bwa

    dbSNP

    download from SRA

    fasta

    fastq

    ftp

    g.vcf

    hpcc

    parallel

    qsub

    reproducing

    rice

    samTools

    samtools

    unix

    Please reload

    Recent Posts

    Reproducing Yang et. al - Aligning

    February 28, 2017

    I'm working on reproducing results from a paper using my methods.

    Make bwa index of Nipponbare v7:

    Turns out there are some fasta formatting mistakes in the nipponbare ref...

    Correct them:

     Prep the file for GATK:

     I processed the raw reads for alignment:

    And aligned (o...

    Read More

    Trimming the reads

    October 6, 2016

    I'll be trimming the reads and removing the adapter sequences today.

    For that ill use Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic & Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics,...

    Read More

    Quality control of the NGS data

    October 2, 2016

    After getting all the files, the first step of analysis will be to assess the quality of the reads generated. 

    FastQC is a good tool for this. I'll be generating reports for each lane separately to check for any lane bias. Also as these are paired end reads (PE) we will...

    Read More
    Please reload

    mansfeld@msu.edu

    Plant Soil Science Bldg 1066 Bogue St., East Lansing Michigan

    • Github
    • twitter
    • linkedin
    • generic-social-link

    ©2016 by Ben Mansfeld. Proudly created with Wix.com