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Raw

Files generate for this project and their location

Raw data location

Maize Dataset

ENA dataset Grab the tsv file from this website and then execute the following command to generate the wget commands

cut -f 7 tsv | more | perl -pe 's/;/\n/g' | xargs -I xx echo "wget ftp://xx"

Download on Nova must be performed on Novadtn

  • Nova: /work/gif/TranscriptomicsWorkshop/severin/Maize
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/004/SRR1573504/SRR1573504_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/004/SRR1573504/SRR1573504_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/005/SRR1573505/SRR1573505_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/005/SRR1573505/SRR1573505_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/006/SRR1573506/SRR1573506_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/006/SRR1573506/SRR1573506_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/007/SRR1573507/SRR1573507_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/007/SRR1573507/SRR1573507_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/008/SRR1573508/SRR1573508_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/008/SRR1573508/SRR1573508_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/009/SRR1573509/SRR1573509_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/009/SRR1573509/SRR1573509_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/000/SRR1573510/SRR1573510_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/000/SRR1573510/SRR1573510_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/001/SRR1573511/SRR1573511_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/001/SRR1573511/SRR1573511_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/002/SRR1573512/SRR1573512_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/002/SRR1573512/SRR1573512_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/003/SRR1573513/SRR1573513_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/003/SRR1573513/SRR1573513_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/004/SRR1573514/SRR1573514_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/004/SRR1573514/SRR1573514_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/005/SRR1573515/SRR1573515_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/005/SRR1573515/SRR1573515_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/006/SRR1573516/SRR1573516_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/006/SRR1573516/SRR1573516_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/007/SRR1573517/SRR1573517_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/007/SRR1573517/SRR1573517_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/008/SRR1573518/SRR1573518_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/008/SRR1573518/SRR1573518_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/009/SRR1573519/SRR1573519_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/009/SRR1573519/SRR1573519_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/000/SRR1573520/SRR1573520_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/000/SRR1573520/SRR1573520_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/001/SRR1573521/SRR1573521_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/001/SRR1573521/SRR1573521_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/002/SRR1573522/SRR1573522_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/002/SRR1573522/SRR1573522_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/003/SRR1573523/SRR1573523_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/003/SRR1573523/SRR1573523_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/004/SRR1573524/SRR1573524_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/004/SRR1573524/SRR1573524_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/005/SRR1573525/SRR1573525_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/005/SRR1573525/SRR1573525_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/006/SRR1573526/SRR1573526_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/006/SRR1573526/SRR1573526_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/007/SRR1573527/SRR1573527_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR157/007/SRR1573527/SRR1573527_2.fastq.gz

Maize Reference - b73

wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/902/167/145/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.fna.gz
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/902/167/145/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.gff.gz

Illumina Reads

BumbleBee dataset

https://drive.google.com/drive/folders/1B8tHao1s_8LLR730iXr1JyQcm0kBm7uL?usp=sharing

Illumina Reads

RNA-Seq data

Genome Assembly

Genome Annotation