STAR manual 2.7.11b

RNA-seq
Author

Songqi Duan

Published

February 4, 2024

仔细阅读了STAR的manual后的记录。

Generating genome indexes

STAR \
  --runThreadN NumberOfThreads
  --runMode genomeGenerate
  --genomeDir /path/to/genomeDir
  --genomeFastaFiles /path/to/genome/fasta
  --sjdbGTFfile /path/to/annotations.gtf
  --sjdbOverhang ReadLength-1
  • sjdbOverhang:In most cases, the default value of 100 will work as well as the ideal value.

Which chromosomes/scaffolds/patches to include?

It is strongly recommended to include major chromosomes (e.g., for human chr1-22,chrX,chrY,chrM,) as well as un-placed and un-localized sca olds. Generally, patches and alternative haplotypes should not be included in the genome.

Reference