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Bowtie2 index

Updated: Dec. 28, 2020 (updated both hs & mm)

Huitian (Yolanda) Diao
bowtie2/2.4.2
HPC Location: /gpfs/group/pipkin/hdiao/ref_resources

Mus Musclus

0. Input genome reference file

Ensembl
Related topic: choice of ensembl genome version

  • Release 102, updated Oct 2020
  • Used softmasked toplevel DNA fasta

Homo Sapiens

0. Input genome reference file

Ensembl](http://useast.ensembl.org/info/data/ftp/index.html)

  • Release 102, updated Oct 2020
  • Used softmasked toplevel DNA fasta

Codes

#!/bin/bash

cd /home/pipkin/references/GRCm38.102
bowtie2-build Mus_musculus.GRCm38.dna_sm.toplevel.fa GRCm38

cd /home/pipkin/references/GRCh38.102
bowtie2-build Homo_sapiens.GRCh38.dna_sm.toplevel.fa GRCh38