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general_ngs.md

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3' DGE from LSP demultiplexing example

bcl2fastq --adapter-stringency 0.9 --barcode-mismatches 0 --fastq-compression-level 4 --min-log-level INFO --minimum-trimmed-read-length 0 --sample-sheet /n/boslfs/INSTRUMENTS/illumina/180604_NB501677_0276_AHVMT2BGX5/SampleSheet.csv --runfolder-dir /n/boslfs/INSTRUMENTS/illumina/180604_NB501677_0276_AHVMT2BGX5 --output-dir /n/boslfs/ANALYSIS/180604_NB501677_0276_AHVMT2BGX5 --processing-threads 8 --no-lane-splitting --mask-short-adapter-reads 0 --use-bases-mask y*,y*,y*,y*

Illumina instrument by FASTQ read name

  • @HWI-Mxxxx or @Mxxxx - MiSeq
  • @Kxxxx - HiSeq 3000(?)/4000
  • @Nxxxx - NextSeq 500/550
  • @Axxxxx - NovaSeq
  • @HWI-Dxxxx - HiSeq 2000/2500
  • AAXX, @HWUSI - GAIIx
  • BCXX = HiSeq v1.5
  • ACXX = HiSeq High-Output v3
  • ANXX = HiSeq High-Output v4
  • ADXX = HiSeq RR v1
  • AMXX, BCXX =HiSeq RR v2
  • ALXX = HiSeqX
  • BGXX, AGXX = High-Output NextSeq
  • AFXX = Mid-Output NextSeq

Illumina BaseSpace CLI

https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview

Miscellaneous

Add text "chr" to #CHROM column of VCF

$ bcftools annotate --rename-chrs <map_file.txt> sample.vcf.gz

map file should contain "old_name new_name" pairs separated by whitespaces, each on a separate line