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YAP
  • Before Start
  • Installation
  • TECH BACKGROUND
    • Barcoding
    • Technology References
    • File Formats
  • Mapping Pipeline
  • Prepare
    • Prepare PlateInfo & bcl2fastq SampleSheet
    • Prepare Mapping Config
      • Prepare Reference Files
  • Demultiplex
  • Mapping
    • Mapping Via Qsub
    • Mapping Via Sbatch
    • Mapping Locally
  • Mapping Form Cell-Level FASTQ Files
  • Summary
  • Mapping Metrics
    • Key Mapping Metrics
    • All Mapping Metrics
  • Generate MCDS
  • Pseudo-bulk
    • Methylome Pseudo-bulk
  • Other
    • FAQ
    • Changelog
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  • Reference FASTA
  • Bismark Reference
  • Gene Annotation GTF (mct only)
  • STAR Reference (mct only)

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  1. Prepare
  2. Prepare Mapping Config

Prepare Reference Files

PreviousPrepare Mapping ConfigNextDemultiplex

Last updated 4 years ago

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The reference files required for making the MappingConfig file is listed below

Reference FASTA

I download reference FASTA from the . For mapping, I will keep all the small contigs to make sure all reads mapped properly, but I usually remove them and only focus on the main chromosomes for further analysis.

Another thing is the lambda DNA spike-in as a non-conversion estimation (we do that), I usually append the with the name chrL to my genome FASTA. You can download the chrL from and append that to your genome.

Bismark Reference

Use bismark to prepare the genome index, see its documentation . Note that we use bowtie2 for snmC-seq and snmCT-seq (that's bismark's default also), and bowtie1 for snm3C-seq ().

Gene Annotation GTF (mct only)

For human and mouse, we usually use . But I do not update GTF throughout the same project. (And the difference between versions probably have little impact on your analysis results.)

STAR Reference (mct only)

Use STAR to prepare its genome index, see its documentation .

UCSC genome browser
lambda genome
NCBI
here
the same as snm3C-seq paper
GENCODE's latest version
here