Try   HackMD

Downloading VGP genomes using awscli

By Tanya Lama

Table of Contents

Install

  1. install or module load anaconda and awscli/1.16.144
    I have installed awscli on Unity following the instructions here: https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html

module load awscli-v2/2.15.53

  1. navigate to the mSorAra bucket. This includes the mito assembly, curated genome assemblies, raw data (genomic_data) and transcriptomic data
    /home/tlama_umass_edu/.local/bin/aws s3 –no-sign-request ls s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/
  2. Copy the uncurated assembly to your local directory.
    /home/tlama_umass_edu/.local/bin/aws s3 –no-sign-request cp s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/mSorAra1.pri.asm.20211103.fasta.gz ./

Appendix and FAQ

Find this document incomplete? Leave a comment!

tags: VGP

where did myoNig go?
not here:
/work/pi_tlama_umass_edu/project_toga/genomes/hg38/trackData
/work/tlama_umass_edu/project_toga/genomes/hg38/trackData

partial here:
/work/tlama_umass_edu/project_bat1k_longevity/analyses/step3_annotation/myoNig_bill

Last changed by 
 
Tanya Lama
As a molecular ecologist I use population genomic data to explore the ecology of species of conservation concern.
0
254

Read more

Uploading raw reads to NCBI SRA database

hackmd-github-sync-badgeBy Tanya Lama

Apr 22, 2025
Configuring Rclone & Backing up to Google Drive/BOX/OneDrive

By Tanya Lama

Oct 28, 2023
Pairwise Sequentially Markovian Coalescent (PSMC) model

By Tanya Lama These scripts were initially run for my dissertation along with other pop gen metrics, but the analysis was eventually abandoned because I didn't have time/support in interpreting the results at the time. This analysis has become much more common among popgen studies so there are likely better resources out there, but if you need to get scripts running in a pinch this should do it for you. Essentially, step one is to take the fasta Canada lynx genome file, align it to a reference (in this case we have Canada lynx but previously had also used Felis Catus) and use the resultant bam file for the PSMC workflow. Only have one genome (e.g., just the reference?) No problem! Just align the raw reads from your assembly to the assembly itself, and use that bam file for the PSMC. I beliee Bentley et al did this for this paper in PNAS and I bet the scripts are decent too: here #This may be easier than converting our .maf to a bam?

Jun 17, 2023
Using Unity cluster

By Tanya Lama

Feb 8, 2023
Read more from Tanya Lama
Published on HackMD